rs4331786

Variant names:

• chr4-38767787-C-T
• rs4331786

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 0.406 in 152,018 control chromosomes in the GnomAD database, including 13,110 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 0.41 (13110 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.805
• Publications: 12 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 (EAS) allele frequency at 95% confidence interval = 0.545 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: 0.406 AC: 61705 AN: 151898 Hom.: 13078 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.406 AC: 61774 AN: 152018 Hom.: 13110 Cov.: 32 AF XY: 0.407 AC XY: 30258 AN XY: 74268

African (AFR) AF: 0.474 AC: 19673 AN: 41466

American (AMR) AF: 0.408 AC: 6236 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1735 AN: 3466

East Asian (EAS) AF: 0.562 AC: 2907 AN: 5172

South Asian (SAS) AF: 0.548 AC: 2647 AN: 4826

European-Finnish (FIN) AF: 0.345 AC: 3633 AN: 10528

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23457 AN: 67962

Other (OTH) AF: 0.468 AC: 987 AN: 2110

Alfa AF: 0.383 Hom.: 34035

Bravo AF: 0.411

Asia WGS AF: 0.522 AC: 1816 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	1.5
DANN	Benign	0.51
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs4331786; hg19: chr4-38769408;