17-71657112-G-T

Variant names:

• chr17-71657112-G-T
• rs4531770

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 0.236 in 148,122 control chromosomes in the GnomAD database, including 5,456 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 (5456 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 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: 0.235 AC: 34849 AN: 148028 Hom.: 5431 Cov.: 27

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.0650

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.189

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.236 AC: 34912 AN: 148122 Hom.: 5456 Cov.: 27 AF XY: 0.240 AC XY: 17309 AN XY: 72154

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.190

Alfa AF: 0.136 Hom.: 1421

Bravo AF: 0.246

Asia WGS AF: 0.365 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4531770; hg19: chr17-69653253; COSMIC: COSV66486449;