chr4-176621822-A-G

Variant names:

• chr4-176621822-A-G
• rs13111989

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 0.226 in 152,120 control chromosomes in the GnomAD database, including 4,486 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 0.23 (4486 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 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: 0.226 AC: 34366 AN: 152002 Hom.: 4492 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.226 AC: 34346 AN: 152120 Hom.: 4486 Cov.: 32 AF XY: 0.225 AC XY: 16716 AN XY: 74352

African (AFR) AF: 0.105 AC: 4369 AN: 41532

American (AMR) AF: 0.218 AC: 3336 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3472

East Asian (EAS) AF: 0.124 AC: 639 AN: 5168

South Asian (SAS) AF: 0.303 AC: 1457 AN: 4810

European-Finnish (FIN) AF: 0.239 AC: 2521 AN: 10554

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.294 AC: 19977 AN: 67996

Other (OTH) AF: 0.267 AC: 563 AN: 2108

Alfa AF: 0.275 Hom.: 22898

Bravo AF: 0.218

Asia WGS AF: 0.182 AC: 633 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.33
DANN	Benign	0.50
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs13111989; hg19: chr4-177542973;