rs10938427

Variant names:

• chr4-46138310-A-G
• rs10938427

Your query was ambiguous. Multiple possible variants found:

• chr4-46138310-A-G
• chr4-46138310-A-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 0.592 in 152,002 control chromosomes in the GnomAD database, including 28,524 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 0.59 (28524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 2 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 = 0.811 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: 0.592 AC: 89866 AN: 151886 Hom.: 28471 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.592 AC: 89975 AN: 152002 Hom.: 28524 Cov.: 32 AF XY: 0.585 AC XY: 43447 AN XY: 74282

African (AFR) AF: 0.818 AC: 33961 AN: 41526

American (AMR) AF: 0.473 AC: 7218 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1384 AN: 3468

East Asian (EAS) AF: 0.308 AC: 1588 AN: 5154

South Asian (SAS) AF: 0.340 AC: 1643 AN: 4832

European-Finnish (FIN) AF: 0.578 AC: 6097 AN: 10550

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.536 AC: 36410 AN: 67898

Other (OTH) AF: 0.537 AC: 1131 AN: 2108

Alfa AF: 0.566 Hom.: 3283

Bravo AF: 0.593

Asia WGS AF: 0.354 AC: 1230 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.6
DANN	Benign	0.52
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10938427; hg19: chr4-46140327;