rs4697926

Variant names:

• chr4-10122943-A-C
• rs4697926

Your query was ambiguous. Multiple possible variants found:

• chr4-10122943-A-C
• chr4-10122943-A-G
• chr4-10122943-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 0.329 in 152,164 control chromosomes in the GnomAD database, including 8,687 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 0.33 (8687 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 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: 0.329 AC: 49993 AN: 152046 Hom.: 8679 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.329 AC: 50025 AN: 152164 Hom.: 8687 Cov.: 33 AF XY: 0.328 AC XY: 24403 AN XY: 74404

African (AFR) AF: 0.224 AC: 9301 AN: 41532

American (AMR) AF: 0.355 AC: 5434 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1385 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1012 AN: 5184

South Asian (SAS) AF: 0.262 AC: 1266 AN: 4824

European-Finnish (FIN) AF: 0.380 AC: 4017 AN: 10576

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.392 AC: 26662 AN: 67978

Other (OTH) AF: 0.338 AC: 714 AN: 2112

Alfa AF: 0.291 Hom.: 1502

Bravo AF: 0.321

Asia WGS AF: 0.241 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.58
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs4697926; hg19: chr4-10124567;