chr3-168930251-T-C

Variant names:

• chr3-168930251-T-C
• rs2201862

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 0.624 in 152,160 control chromosomes in the GnomAD database, including 31,532 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 0.62 (31532 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 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: 0.624 AC: 94806 AN: 152040 Hom.: 31478 Cov.: 33

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.624 AC: 94913 AN: 152160 Hom.: 31532 Cov.: 33 AF XY: 0.629 AC XY: 46788 AN XY: 74374

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.559

Alfa AF: 0.564 Hom.: 3172

Bravo AF: 0.635

Asia WGS AF: 0.689 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2201862; hg19: chr3-168648039;