rs1553748

Variant names:

• chr17-48484319-A-G
• rs1553748

Your query was ambiguous. Multiple possible variants found:

• chr17-48484319-A-G
• chr17-48484319-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 0.732 in 152,142 control chromosomes in the GnomAD database, including 43,475 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 (43475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 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: 0.732 AC: 111299 AN: 152024 Hom.: 43465 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.732 AC: 111331 AN: 152142 Hom.: 43475 Cov.: 32 AF XY: 0.736 AC XY: 54790 AN XY: 74400

African (AFR) AF: 0.435 AC: 18055 AN: 41464

American (AMR) AF: 0.806 AC: 12317 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2767 AN: 3470

East Asian (EAS) AF: 0.877 AC: 4547 AN: 5182

South Asian (SAS) AF: 0.733 AC: 3532 AN: 4816

European-Finnish (FIN) AF: 0.935 AC: 9922 AN: 10616

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57661 AN: 67992

Other (OTH) AF: 0.744 AC: 1569 AN: 2108

Alfa AF: 0.815 Hom.: 27395

Bravo AF: 0.711

Asia WGS AF: 0.755 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.83
DANN	Benign	0.58
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1553748; hg19: chr17-46561681;