17-71657112-G-T

Variant names:

• chr17-71657112-G-T
• rs4531770

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 0.236 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.428 AC: 16796 AN: 39206

American (AMR) AF: 0.169 AC: 2533 AN: 14954

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 445 AN: 3454

East Asian (EAS) AF: 0.436 AC: 2170 AN: 4974

South Asian (SAS) AF: 0.310 AC: 1441 AN: 4652

European-Finnish (FIN) AF: 0.189 AC: 1881 AN: 9970

Middle Eastern (MID) AF: 0.200 AC: 56 AN: 280

European-Non Finnish (NFE) AF: 0.135 AC: 9138 AN: 67660

Other (OTH) AF: 0.190 AC: 393 AN: 2064

Alfa AF: 0.153 Hom.: 3170

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
PhyloP100		-0.71

Splicing

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

Other links and lift over

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