Variant 17-40130817-G-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_001365919.1(MSL1):c.1376-720G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 152,320 control chromosomes in the GnomAD database, including 49 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 0.018 ( 49 hom., cov: 32)

Exomes 𝑓: 0.050 ( 0 hom. )

Consequence

MSL1
NM_001365919.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.75

Variant links:

Genes affected

MSL1 (HGNC:27905): (MSL complex subunit 1) Predicted to enable chromatin binding activity. Involved in histone H4-K16 acetylation. Located in nucleoplasm. Part of MSL complex. [provided by Alliance of Genome Resources, Apr 2022]

MSL1 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=-0.51).

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency = 0.0625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
MSL1	NM_001365919.1 linkuse as main transcript	c.1376-720G>C	intron_variant	ENST00000398532.9
MSL1	NM_001012241.2 linkuse as main transcript	c.587-720G>C	intron_variant
MSL1	NM_001365920.1 linkuse as main transcript	c.1375+1190G>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
MSL1	ENST00000398532.9 linkuse as main transcript	c.1376-720G>C	intron_variant	1	NM_001365919.1	P3	Q68DK7-1
MSL1	ENST00000579565.5 linkuse as main transcript	c.587-720G>C	intron_variant	1			Q68DK7-3
MSL1	ENST00000578648.5 linkuse as main transcript	c.1375+1190G>C	intron_variant	5		A1
MSL1	ENST00000582884.5 linkuse as main transcript	c.398-403G>C	intron_variant, NMD_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0182

AC:

2774

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00524

Gnomad AMI

AF:

0.0702

Gnomad AMR

AF:

0.0123

Gnomad ASJ

AF:

0.0144

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00787

Gnomad FIN

AF:

0.00886

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0306

Gnomad OTH

AF:

0.0153

GnomAD4 exome

AF:

0.0500

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0625

GnomAD4 genome

AF:

0.0182

AC:

2774

AN:

152300

Hom.:

Cov.:

AF XY:

0.0173

AC XY:

1287

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00522

Gnomad4 AMR

AF:

0.0123

Gnomad4 ASJ

AF:

0.0144

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00787

Gnomad4 FIN

AF:

0.00886

Gnomad4 NFE

AF:

0.0307

Gnomad4 OTH

AF:

0.0152

Alfa

AF:

0.0154

Hom.:

Bravo

AF:

0.0185

Asia WGS

AF:

0.00375

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Benign

0.80

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