chr7-120785764-G-A

Variant names:

• chr7-120785764-G-A
• rs41620

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.585 AC: 24226 AN: 41442

American (AMR) AF: 0.795 AC: 12145 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2798 AN: 3470

East Asian (EAS) AF: 0.930 AC: 4792 AN: 5154

South Asian (SAS) AF: 0.884 AC: 4258 AN: 4816

European-Finnish (FIN) AF: 0.622 AC: 6563 AN: 10556

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.729 AC: 49549 AN: 67964

Other (OTH) AF: 0.729 AC: 1534 AN: 2104

Alfa AF: 0.734 Hom.: 58100

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
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs41620; hg19: chr7-120425818;