rs2251830

Variant names:

• chr6-31049201-C-A
• rs2251830

Your query was ambiguous. Multiple possible variants found:

• chr6-31049201-C-A
• chr6-31049201-C-G
• chr6-31049201-C-T

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 0.466 in 151,670 control chromosomes in the GnomAD database, including 17,215 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 (17215 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 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: 0.466 AC: 70579 AN: 151554 Hom.: 17179 Cov.: 30

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.466 AC: 70658 AN: 151670 Hom.: 17215 Cov.: 30 AF XY: 0.457 AC XY: 33844 AN XY: 74094

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.495

Alfa AF: 0.434 Hom.: 8192

Bravo AF: 0.477

Asia WGS AF: 0.410 AC: 1428 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2251830; hg19: chr6-31016978;