rs1038813

Variant names:

• chr4-171230669-G-A
• rs1038813

Your query was ambiguous. Multiple possible variants found:

• chr4-171230669-G-A
• chr4-171230669-G-C
• chr4-171230669-G-T

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 0.888 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.862 AC: 35793 AN: 41520

American (AMR) AF: 0.924 AC: 14116 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3070 AN: 3470

East Asian (EAS) AF: 0.932 AC: 4822 AN: 5172

South Asian (SAS) AF: 0.923 AC: 4450 AN: 4820

European-Finnish (FIN) AF: 0.926 AC: 9830 AN: 10616

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60131 AN: 68000

Other (OTH) AF: 0.893 AC: 1884 AN: 2110

Alfa AF: 0.886 Hom.: 7727

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1038813; hg19: chr4-172151820;