rs2431866

Variant names:

• chr19-7570985-C-A
• rs2431866

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 0.126 in 152,090 control chromosomes in the GnomAD database, including 1,661 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 0.13 (1661 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 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: 0.126 AC: 19134 AN: 151972 Hom.: 1656 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0832

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0962

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.126 AC: 19161 AN: 152090 Hom.: 1661 Cov.: 32 AF XY: 0.121 AC XY: 9025 AN XY: 74358

African (AFR) AF: 0.232 AC: 9593 AN: 41438

American (AMR) AF: 0.0836 AC: 1275 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0832 AC: 289 AN: 3472

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5176

South Asian (SAS) AF: 0.0162 AC: 78 AN: 4818

European-Finnish (FIN) AF: 0.0712 AC: 754 AN: 10596

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0961 AC: 6540 AN: 68020

Other (OTH) AF: 0.125 AC: 263 AN: 2112

Alfa AF: 0.100 Hom.: 1552

Bravo AF: 0.134

Asia WGS AF: 0.0230 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
DANN	Benign	0.39
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2431866; hg19: chr19-7635871;