chr4-163322228-A-T

Variant names:

• chr4-163322228-A-T
• rs6832644

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 0.284 in 152,110 control chromosomes in the GnomAD database, including 6,712 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 0.28 (6712 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 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: 0.284 AC: 43149 AN: 151992 Hom.: 6714 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.284 AC: 43154 AN: 152110 Hom.: 6712 Cov.: 33 AF XY: 0.290 AC XY: 21577 AN XY: 74346

African (AFR) AF: 0.194 AC: 8064 AN: 41518

American (AMR) AF: 0.289 AC: 4427 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 928 AN: 3468

East Asian (EAS) AF: 0.592 AC: 3062 AN: 5170

South Asian (SAS) AF: 0.324 AC: 1563 AN: 4818

European-Finnish (FIN) AF: 0.438 AC: 4620 AN: 10556

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19617 AN: 67970

Other (OTH) AF: 0.279 AC: 591 AN: 2116

Alfa AF: 0.276 Hom.: 741

Bravo AF: 0.272

Asia WGS AF: 0.398 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.2
DANN	Benign	0.75
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs6832644; hg19: chr4-164243380;