rs7762544

chr6-41411577-G-Achr6-41411577-G-Cchr6-41411577-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.812 in 152,138 control chromosomes in the GnomAD database, including 50,349 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 0.81 (50349 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123427 AN: 152020 Hom.: 50299 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.769

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.812 AC: 123537 AN: 152138 Hom.: 50349 Cov.: 31 AF XY: 0.815 AC XY: 60586 AN XY: 74360

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.771

Alfa AF: 0.809 Hom.: 13382

Bravo AF: 0.807

Asia WGS AF: 0.911 AC: 3170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.7
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7762544; hg19: chr6-41379315;