rs17544159

Variant names:

• chr6-53265722-A-C
• rs17544159

Your query was ambiguous. Multiple possible variants found:

• chr6-53265722-A-C
• chr6-53265722-A-T

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 0.0495 in 152,282 control chromosomes in the GnomAD database, including 257 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 0.049 (257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.138 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: 0.0496 AC: 7543 AN: 152164 Hom.: 258 Cov.: 32

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0530

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.0920

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0495 AC: 7535 AN: 152282 Hom.: 257 Cov.: 32 AF XY: 0.0485 AC XY: 3612 AN XY: 74458

African (AFR) AF: 0.0171 AC: 711 AN: 41574

American (AMR) AF: 0.0528 AC: 807 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0619 AC: 215 AN: 3472

East Asian (EAS) AF: 0.0918 AC: 475 AN: 5172

South Asian (SAS) AF: 0.146 AC: 706 AN: 4820

European-Finnish (FIN) AF: 0.0127 AC: 135 AN: 10616

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0629 AC: 4276 AN: 68008

Other (OTH) AF: 0.0633 AC: 134 AN: 2116

Alfa AF: 0.0181 Hom.: 4

Bravo AF: 0.0502

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.43
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs17544159; hg19: chr6-53130520;