rs2677247

Variant names:

• chr3-103731747-A-C
• rs2677247

Your query was ambiguous. Multiple possible variants found:

• chr3-103731747-A-C
• chr3-103731747-A-G
• chr3-103731747-A-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 0.472 in 151,912 control chromosomes in the GnomAD database, including 19,585 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 0.47 (19585 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 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: 0.473 AC: 71772 AN: 151796 Hom.: 19586 Cov.: 33

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.472 AC: 71768 AN: 151912 Hom.: 19585 Cov.: 33 AF XY: 0.468 AC XY: 34744 AN XY: 74232

African (AFR) AF: 0.220 AC: 9114 AN: 41498

American (AMR) AF: 0.503 AC: 7675 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2411 AN: 3466

East Asian (EAS) AF: 0.154 AC: 799 AN: 5178

South Asian (SAS) AF: 0.369 AC: 1778 AN: 4824

European-Finnish (FIN) AF: 0.607 AC: 6402 AN: 10540

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41725 AN: 67844

Other (OTH) AF: 0.513 AC: 1082 AN: 2110

Alfa AF: 0.496 Hom.: 18401

Bravo AF: 0.453

Asia WGS AF: 0.232 AC: 806 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.33
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2677247; hg19: chr3-103450591;