chr3-161506750-G-A

Variant names:

• chr3-161506750-G-A
• rs7644500

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 0.174 in 151,956 control chromosomes in the GnomAD database, including 3,099 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 0.17 (3099 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 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: 0.174 AC: 26457 AN: 151834 Hom.: 3086 Cov.: 31

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.174 AC: 26514 AN: 151956 Hom.: 3099 Cov.: 31 AF XY: 0.175 AC XY: 12964 AN XY: 74276

African (AFR) AF: 0.329 AC: 13608 AN: 41422

American (AMR) AF: 0.121 AC: 1840 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3468

East Asian (EAS) AF: 0.120 AC: 620 AN: 5148

South Asian (SAS) AF: 0.309 AC: 1485 AN: 4802

European-Finnish (FIN) AF: 0.101 AC: 1066 AN: 10568

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7144 AN: 67982

Other (OTH) AF: 0.157 AC: 331 AN: 2104

Alfa AF: 0.117 Hom.: 807

Bravo AF: 0.176

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.29
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7644500; hg19: chr3-161224538;