rs41620

Variant names:

• chr7-120785764-G-A
• rs41620

Your query was ambiguous. Multiple possible variants found:

• chr7-120785764-G-A
• chr7-120785764-G-C

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 0.703 in 151,992 control chromosomes in the GnomAD database, including 38,130 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 0.70 (38130 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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: 0.703 AC: 106745 AN: 151872 Hom.: 38117 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.879

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.703 AC: 106800 AN: 151992 Hom.: 38130 Cov.: 31 AF XY: 0.704 AC XY: 52318 AN XY: 74278

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.729

Alfa AF: 0.737 Hom.: 38824

Bravo AF: 0.709

Asia WGS AF: 0.822 AC: 2857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41620; hg19: chr7-120425818;