rs1017024

Variant names:

• chr14-71172644-C-T
• rs1017024

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 0.164 in 152,130 control chromosomes in the GnomAD database, including 2,136 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 0.16 (2136 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 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: 0.164 AC: 24985 AN: 152012 Hom.: 2135 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0616

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.164 AC: 25002 AN: 152130 Hom.: 2136 Cov.: 32 AF XY: 0.163 AC XY: 12094 AN XY: 74364

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0618

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.165

Alfa AF: 0.178 Hom.: 510

Bravo AF: 0.158

Asia WGS AF: 0.170 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.88
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1017024; hg19: chr14-71639361;