rs7648041

Variant names:

• chr3-122181001-C-T
• rs7648041

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 0.234 in 152,110 control chromosomes in the GnomAD database, including 4,626 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 0.23 (4626 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 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: 0.234 AC: 35577 AN: 151992 Hom.: 4622 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.00865

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.234 AC: 35595 AN: 152110 Hom.: 4626 Cov.: 31 AF XY: 0.232 AC XY: 17285 AN XY: 74358

African (AFR) AF: 0.164 AC: 6821 AN: 41484

American (AMR) AF: 0.210 AC: 3206 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3466

East Asian (EAS) AF: 0.00867 AC: 45 AN: 5188

South Asian (SAS) AF: 0.185 AC: 889 AN: 4818

European-Finnish (FIN) AF: 0.311 AC: 3291 AN: 10578

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19432 AN: 67974

Other (OTH) AF: 0.242 AC: 511 AN: 2112

Alfa AF: 0.269 Hom.: 24272

Bravo AF: 0.225

Asia WGS AF: 0.126 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.39
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7648041; hg19: chr3-121899848;