rs17084868

Variant names:

• chr6-154000799-A-C
• rs17084868

Your query was ambiguous. Multiple possible variants found:

• chr6-154000799-A-C
• chr6-154000799-A-G

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 0.164 in 152,228 control chromosomes in the GnomAD database, including 2,634 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 (2634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 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: 0.165 AC: 25050 AN: 152108 Hom.: 2638 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.164 AC: 25037 AN: 152228 Hom.: 2634 Cov.: 32 AF XY: 0.176 AC XY: 13085 AN XY: 74416

African (AFR) AF: 0.0533 AC: 2215 AN: 41576

American (AMR) AF: 0.256 AC: 3914 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2020 AN: 5180

South Asian (SAS) AF: 0.363 AC: 1746 AN: 4812

European-Finnish (FIN) AF: 0.233 AC: 2461 AN: 10580

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

European-Non Finnish (NFE) AF: 0.168 AC: 11419 AN: 67998

Other (OTH) AF: 0.174 AC: 369 AN: 2116

Alfa AF: 0.149 Hom.: 296

Bravo AF: 0.155

Asia WGS AF: 0.368 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.6
DANN	Benign	0.77
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs17084868; hg19: chr6-154321934;