rs7762544

Variant names:

• chr6-41411577-G-A
• rs7762544

Your query was ambiguous. Multiple possible variants found:

• chr6-41411577-G-A
• chr6-41411577-G-C
• chr6-41411577-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;