rs17641380

Variant names:

• chr4-44159772-T-C
• rs17641380

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 0.183 in 151,600 control chromosomes in the GnomAD database, including 2,891 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 0.18 (2891 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 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: 0.183 AC: 27656 AN: 151482 Hom.: 2885 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.183 AC: 27680 AN: 151600 Hom.: 2891 Cov.: 31 AF XY: 0.188 AC XY: 13889 AN XY: 74068

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.188

Alfa AF: 0.181 Hom.: 1407

Bravo AF: 0.189

Asia WGS AF: 0.340 AC: 1179 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17641380; hg19: chr4-44161789;