rs7224488

Variant names:

• chr17-56791264-A-C
• rs7224488

Your query was ambiguous. Multiple possible variants found:

• chr17-56791264-A-C
• chr17-56791264-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 0.756 in 151,930 control chromosomes in the GnomAD database, including 43,732 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 0.76 (43732 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 4 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 = 0.813 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: 0.756 AC: 114827 AN: 151812 Hom.: 43727 Cov.: 30

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.756 AC: 114876 AN: 151930 Hom.: 43732 Cov.: 30 AF XY: 0.757 AC XY: 56236 AN XY: 74262

African (AFR) AF: 0.683 AC: 28286 AN: 41410

American (AMR) AF: 0.786 AC: 11996 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2757 AN: 3468

East Asian (EAS) AF: 0.834 AC: 4306 AN: 5166

South Asian (SAS) AF: 0.747 AC: 3601 AN: 4820

European-Finnish (FIN) AF: 0.716 AC: 7536 AN: 10530

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53781 AN: 67960

Other (OTH) AF: 0.784 AC: 1653 AN: 2108

Alfa AF: 0.778 Hom.: 184220

Bravo AF: 0.758

Asia WGS AF: 0.756 AC: 2629 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	4.1
DANN	Benign	0.63
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs7224488; hg19: chr17-54868625;