chr17-48539657-A-G

Variant names:

• chr17-48539657-A-G
• rs6504340

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 0.73 in 152,102 control chromosomes in the GnomAD database, including 41,535 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 0.73 (41535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 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: 0.730 AC: 110982 AN: 151984 Hom.: 41494 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.730 AC: 111075 AN: 152102 Hom.: 41535 Cov.: 32 AF XY: 0.734 AC XY: 54568 AN XY: 74344

African (AFR) AF: 0.563 AC: 23339 AN: 41454

American (AMR) AF: 0.805 AC: 12313 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2641 AN: 3470

East Asian (EAS) AF: 0.915 AC: 4744 AN: 5184

South Asian (SAS) AF: 0.847 AC: 4080 AN: 4818

European-Finnish (FIN) AF: 0.775 AC: 8202 AN: 10588

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53336 AN: 67982

Other (OTH) AF: 0.741 AC: 1564 AN: 2112

Alfa AF: 0.775 Hom.: 184721

Bravo AF: 0.726

Asia WGS AF: 0.840 AC: 2920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.59
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs6504340; hg19: chr17-46617019;