Variant chr6-97151736-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001350599.2(MMS22L):c.3482+35A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 1,533,606 control chromosomes in the GnomAD database, including 32,324 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.19 ( 3018 hom., cov: 32)

Exomes 𝑓: 0.20 ( 29306 hom. )

Consequence

MMS22L
NM_001350599.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.78

Variant links:

Genes affected

MMS22L (HGNC:21475): (MMS22 like, DNA repair protein) The protein encoded by this gene forms a complex with tonsoku-like, DNA repair protein (TONSL), and this complex recognizes and repairs DNA double-strand breaks at sites of stalled or collapsed replication forks. The encoded protein also can bind with the histone-associated protein NFKBIL2 to help regulate the chromatin state at stalled replication forks. Finally, this gene appears to be overexpressed in most lung and esophageal cancers. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2017]

MMS22L links:

MMS22L (HGNC:):

MMS22L links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MMS22L	NM_001350599.2 linkuse as main transcript	c.3482+35A>G		intron_variant		ENST00000683635.1	NP_001337528.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MMS22L	ENST00000683635.1 linkuse as main transcript	c.3482+35A>G	intron_variant			NM_001350599.2	ENSP00000508046.1	Q6ZRQ5
MMS22L	ENST00000275053.8 linkuse as main transcript	c.3482+35A>G	intron_variant		2		ENSP00000275053.4	Q6ZRQ5
MMS22L	ENST00000369251.6 linkuse as main transcript	c.3362+35A>G	intron_variant		2		ENSP00000358254.2	E2QRD4
MMS22L	ENST00000514790.1 linkuse as main transcript	n.176A>G	non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes

AF:

0.185

AC:

28151

AN:

152062

Hom.:

3006

Cov.:

show subpopulations

Gnomad AFR

AF:

0.138

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.149

Gnomad EAS

AF:

0.519

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.206

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.179

Gnomad OTH

AF:

0.170

GnomAD3 exomes

AF:

0.226

AC:

56328

AN:

249248

Hom.:

7656

AF XY:

0.222

AC XY:

29877

AN XY:

134666

show subpopulations

Gnomad AFR exome

AF:

0.138

Gnomad AMR exome

AF:

0.288

Gnomad ASJ exome

AF:

0.155

Gnomad EAS exome

AF:

0.524

Gnomad SAS exome

AF:

0.234

Gnomad FIN exome

AF:

0.209

Gnomad NFE exome

AF:

0.180

Gnomad OTH exome

AF:

0.205

GnomAD4 exome

AF:

0.198

AC:

273164

AN:

1381426

Hom.:

29306

Cov.:

AF XY:

0.198

AC XY:

136933

AN XY:

691672

show subpopulations

Gnomad4 AFR exome

AF:

0.136

Gnomad4 AMR exome

AF:

0.275

Gnomad4 ASJ exome

AF:

0.155

Gnomad4 EAS exome

AF:

0.477

Gnomad4 SAS exome

AF:

0.233

Gnomad4 FIN exome

AF:

0.211

Gnomad4 NFE exome

AF:

0.183

Gnomad4 OTH exome

AF:

0.210

GnomAD4 genome

AF:

0.185

AC:

28178

AN:

152180

Hom.:

3018

Cov.:

AF XY:

0.188

AC XY:

14000

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.138

Gnomad4 AMR

AF:

0.206

Gnomad4 ASJ

AF:

0.149

Gnomad4 EAS

AF:

0.520

Gnomad4 SAS

AF:

0.241

Gnomad4 FIN

AF:

0.206

Gnomad4 NFE

AF:

0.179

Gnomad4 OTH

AF:

0.180

Alfa

AF:

0.183

Hom.:

5189

Bravo

AF:

0.190

Asia WGS

AF:

0.405

AC:

1408

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

0.038

DANN

Benign

0.70

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over