rs17084870

Variant names:

• chr6-154001443-G-T
• rs17084870

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 0.2 in 152,088 control chromosomes in the GnomAD database, including 3,311 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 0.20 (3311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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: 0.200 AC: 30460 AN: 151970 Hom.: 3314 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.200 AC: 30467 AN: 152088 Hom.: 3311 Cov.: 32 AF XY: 0.210 AC XY: 15647 AN XY: 74346

African (AFR) AF: 0.178 AC: 7399 AN: 41484

American (AMR) AF: 0.268 AC: 4092 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3468

East Asian (EAS) AF: 0.388 AC: 2008 AN: 5176

South Asian (SAS) AF: 0.363 AC: 1751 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2455 AN: 10570

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11449 AN: 67964

Other (OTH) AF: 0.200 AC: 421 AN: 2110

Alfa AF: 0.189 Hom.: 482

Bravo AF: 0.195

Asia WGS AF: 0.375 AC: 1304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.088
DANN	Benign	0.46
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs17084870; hg19: chr6-154322578; COSMIC: COSV107167861;