chr4-169979868-C-T

Variant names:

• chr4-169979868-C-T
• rs10033615

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 0.241 in 152,176 control chromosomes in the GnomAD database, including 4,831 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 0.24 (4831 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 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: 0.241 AC: 36706 AN: 152058 Hom.: 4832 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.241 AC: 36709 AN: 152176 Hom.: 4831 Cov.: 33 AF XY: 0.247 AC XY: 18370 AN XY: 74386

African (AFR) AF: 0.218 AC: 9051 AN: 41516

American (AMR) AF: 0.288 AC: 4401 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 748 AN: 3470

East Asian (EAS) AF: 0.615 AC: 3184 AN: 5174

South Asian (SAS) AF: 0.241 AC: 1165 AN: 4826

European-Finnish (FIN) AF: 0.277 AC: 2933 AN: 10574

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14367 AN: 68000

Other (OTH) AF: 0.259 AC: 546 AN: 2112

Alfa AF: 0.223 Hom.: 11255

Bravo AF: 0.246

Asia WGS AF: 0.420 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.46
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10033615; hg19: chr4-170901019;