rs2625955

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;