rs4697924

Variant names:

• chr4-10122615-T-C
• rs4697924

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 0.325 in 152,098 control chromosomes in the GnomAD database, including 8,573 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 (8573 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49460 AN: 151980 Hom.: 8566 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.325 AC: 49485 AN: 152098 Hom.: 8573 Cov.: 33 AF XY: 0.324 AC XY: 24130 AN XY: 74368

African (AFR) AF: 0.213 AC: 8814 AN: 41468

American (AMR) AF: 0.353 AC: 5399 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1387 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1004 AN: 5170

South Asian (SAS) AF: 0.263 AC: 1271 AN: 4828

European-Finnish (FIN) AF: 0.380 AC: 4026 AN: 10592

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26638 AN: 67964

Other (OTH) AF: 0.336 AC: 710 AN: 2114

Alfa AF: 0.351 Hom.: 1569

Bravo AF: 0.317

Asia WGS AF: 0.237 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.60
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4697924; hg19: chr4-10124239;