rs1038813

chr4-171230669-G-Achr4-171230669-G-Cchr4-171230669-G-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 0.888 in 152,192 control chromosomes in the GnomAD database, including 60,101 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 0.89 (60101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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: 0.888 AC: 135049 AN: 152074 Hom.: 60053 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.888 AC: 135153 AN: 152192 Hom.: 60101 Cov.: 32 AF XY: 0.892 AC XY: 66368 AN XY: 74410

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.924

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.893

Alfa AF: 0.887 Hom.: 7444

Bravo AF: 0.887

Asia WGS AF: 0.910 AC: 3164 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.4
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1038813; hg19: chr4-172151820;