chr17-31705401-C-T

Variant names:

• chr17-31705401-C-T
• rs1551355

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 0.173 in 152,136 control chromosomes in the GnomAD database, including 2,774 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 0.17 (2774 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 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: 0.173 AC: 26281 AN: 152018 Hom.: 2772 Cov.: 32

Gnomad AFR AF: 0.0462

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.0727

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.173 AC: 26286 AN: 152136 Hom.: 2774 Cov.: 32 AF XY: 0.172 AC XY: 12814 AN XY: 74358

African (AFR) AF: 0.0461 AC: 1914 AN: 41528

American (AMR) AF: 0.196 AC: 2989 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3470

East Asian (EAS) AF: 0.0726 AC: 376 AN: 5176

South Asian (SAS) AF: 0.165 AC: 796 AN: 4822

European-Finnish (FIN) AF: 0.257 AC: 2718 AN: 10560

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15916 AN: 67992

Other (OTH) AF: 0.178 AC: 376 AN: 2112

Alfa AF: 0.225 Hom.: 5591

Bravo AF: 0.163

Asia WGS AF: 0.106 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.50
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1551355; hg19: chr17-30032420;