4-182888119-C-T

Variant names:

• chr4-182888119-C-T
• rs17271644

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.503 in 151,844 control chromosomes in the GnomAD database, including 20,516 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 0.50 (20516 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 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: 0.503 AC: 76390 AN: 151726 Hom.: 20500 Cov.: 31

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.503 AC: 76452 AN: 151844 Hom.: 20516 Cov.: 31 AF XY: 0.501 AC XY: 37153 AN XY: 74194

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.475

Alfa AF: 0.429 Hom.: 24692

Bravo AF: 0.514

Asia WGS AF: 0.485 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17271644; hg19: chr4-183809272;