rs275679

Variant names:

• chr3-148650516-G-C
• rs275679

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 0.215 in 152,116 control chromosomes in the GnomAD database, including 3,637 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 0.21 (3637 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 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: 0.215 AC: 32611 AN: 151998 Hom.: 3630 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.215 AC: 32644 AN: 152116 Hom.: 3637 Cov.: 32 AF XY: 0.211 AC XY: 15681 AN XY: 74382

African (AFR) AF: 0.239 AC: 9898 AN: 41480

American (AMR) AF: 0.168 AC: 2563 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1116 AN: 3472

East Asian (EAS) AF: 0.129 AC: 667 AN: 5170

South Asian (SAS) AF: 0.192 AC: 925 AN: 4816

European-Finnish (FIN) AF: 0.138 AC: 1460 AN: 10580

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.222 AC: 15093 AN: 68008

Other (OTH) AF: 0.244 AC: 516 AN: 2112

Alfa AF: 0.214 Hom.: 455

Bravo AF: 0.215

Asia WGS AF: 0.152 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.83
DANN	Benign	0.49
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs275679; hg19: chr3-148368303;