rs5008830

Variant names:

• chr3-122311615-G-A
• rs5008830

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 0.124 in 152,072 control chromosomes in the GnomAD database, including 1,425 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 0.12 (1425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.930
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.17 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: 0.124 AC: 18790 AN: 151954 Hom.: 1424 Cov.: 32

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.124 AC: 18792 AN: 152072 Hom.: 1425 Cov.: 32 AF XY: 0.124 AC XY: 9205 AN XY: 74336

African (AFR) AF: 0.0523 AC: 2168 AN: 41486

American (AMR) AF: 0.144 AC: 2201 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3468

East Asian (EAS) AF: 0.0277 AC: 144 AN: 5192

South Asian (SAS) AF: 0.180 AC: 865 AN: 4812

European-Finnish (FIN) AF: 0.140 AC: 1474 AN: 10562

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10438 AN: 67968

Other (OTH) AF: 0.160 AC: 338 AN: 2110

Alfa AF: 0.135 Hom.: 252

Bravo AF: 0.120

Asia WGS AF: 0.112 AC: 390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.96
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs5008830; hg19: chr3-122030462; COSMIC: COSV107175888;