rs1431935

Positions:

• chr4-186796763-C-A
• chr4-186796763-C-G
• chr4-186796763-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 0.39 in 151,792 control chromosomes in the GnomAD database, including 12,876 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 0.39 (12876 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59206 AN: 151674 Hom.: 12876 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.390 AC: 59213 AN: 151792 Hom.: 12876 Cov.: 32 AF XY: 0.389 AC XY: 28874 AN XY: 74166

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.434

Alfa AF: 0.436 Hom.: 4659

Bravo AF: 0.377

Asia WGS AF: 0.345 AC: 1201 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	10
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1431935; hg19: chr4-187717917;