rs2625955

Variant names:

• chr3-129527956-C-A
• rs2625955

Your query was ambiguous. Multiple possible variants found:

• chr3-129527956-C-A
• chr3-129527956-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.38 in 152,140 control chromosomes in the GnomAD database, including 17,957 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 0.38 (17957 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 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: 0.380 AC: 57748 AN: 152022 Hom.: 17894 Cov.: 33

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.0706

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.380 AC: 57876 AN: 152140 Hom.: 17957 Cov.: 33 AF XY: 0.380 AC XY: 28288 AN XY: 74400

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.0706

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.347

Alfa AF: 0.254 Hom.: 1871

Bravo AF: 0.419

Asia WGS AF: 0.506 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.097
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2625955; hg19: chr3-129246799;