Variant rs904773 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_001447.2(MT1L):n.130+99C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 416,980 control chromosomes in the GnomAD database, including 132,533 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 0.80 ( 49136 hom., cov: 33)

Exomes 𝑓: 0.79 ( 83397 hom. )

Consequence

MT1L
NR_001447.2 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.16

Variant links:

Genes affected

(HGNC:):

links:

MT1L (HGNC:7404): (metallothionein 1L (pseudogene)) Predicted to enable zinc ion binding activity. Involved in cellular response to zinc ion. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MT1L 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MT1L	NR_001447.2 linkuse as main transcript	n.130+99C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
	ENST00000565768.3 linkuse as main transcript	n.168+99C>A	intron_variant, non_coding_transcript_variant	1
MT1L	ENST00000566367.2 linkuse as main transcript	n.28+99C>A	intron_variant, non_coding_transcript_variant
	ENST00000686205.1 linkuse as main transcript	n.146+99C>A	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.802

AC:

121955

AN:

152038

Hom.:

49095

Cov.:

show subpopulations

Gnomad AFR

AF:

0.831

Gnomad AMI

AF:

0.847

Gnomad AMR

AF:

0.740

Gnomad ASJ

AF:

0.795

Gnomad EAS

AF:

0.753

Gnomad SAS

AF:

0.818

Gnomad FIN

AF:

0.736

Gnomad MID

AF:

0.823

Gnomad NFE

AF:

0.811

Gnomad OTH

AF:

0.806

GnomAD4 exome

AF:

0.792

AC:

209822

AN:

264826

Hom.:

83397

AF XY:

0.795

AC XY:

120339

AN XY:

151444

show subpopulations

Gnomad4 AFR exome

AF:

0.836

Gnomad4 AMR exome

AF:

0.681

Gnomad4 ASJ exome

AF:

0.803

Gnomad4 EAS exome

AF:

0.760

Gnomad4 SAS exome

AF:

0.807

Gnomad4 FIN exome

AF:

0.743

Gnomad4 NFE exome

AF:

0.809

Gnomad4 OTH exome

AF:

0.802

GnomAD4 genome

AF:

0.802

AC:

122049

AN:

152154

Hom.:

49136

Cov.:

AF XY:

0.798

AC XY:

59314

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.832

Gnomad4 AMR

AF:

0.740

Gnomad4 ASJ

AF:

0.795

Gnomad4 EAS

AF:

0.753

Gnomad4 SAS

AF:

0.817

Gnomad4 FIN

AF:

0.736

Gnomad4 NFE

AF:

0.811

Gnomad4 OTH

AF:

0.806

Alfa

AF:

0.809

Hom.:

12168

Bravo

AF:

0.800

Asia WGS

AF:

0.786

AC:

2731

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.34

DANN

Benign

0.30

Splicing

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