rs7648592

Variant names:

• chr3-135856237-G-A
• rs7648592

Your query was ambiguous. Multiple possible variants found:

• chr3-135856237-G-A
• chr3-135856237-G-T

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 0.192 in 152,050 control chromosomes in the GnomAD database, including 2,953 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 0.19 (2953 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 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: 0.192 AC: 29207 AN: 151932 Hom.: 2951 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.192 AC: 29222 AN: 152050 Hom.: 2953 Cov.: 32 AF XY: 0.193 AC XY: 14363 AN XY: 74324

African (AFR) AF: 0.189 AC: 7828 AN: 41494

American (AMR) AF: 0.135 AC: 2060 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 616 AN: 3472

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5182

South Asian (SAS) AF: 0.156 AC: 747 AN: 4802

European-Finnish (FIN) AF: 0.278 AC: 2935 AN: 10560

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14357 AN: 67944

Other (OTH) AF: 0.187 AC: 394 AN: 2112

Alfa AF: 0.200 Hom.: 9734

Bravo AF: 0.181

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.3
DANN	Benign	0.58
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7648592; hg19: chr3-135575079;