rs4790953

Variant names:

• chr17-65230912-A-C
• rs4790953

Your query was ambiguous. Multiple possible variants found:

• chr17-65230912-A-C
• chr17-65230912-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 0.166 in 152,106 control chromosomes in the GnomAD database, including 3,657 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 0.17 (3657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.448
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.166 AC: 25239 AN: 151988 Hom.: 3636 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.0791

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.166 AC: 25316 AN: 152106 Hom.: 3657 Cov.: 32 AF XY: 0.168 AC XY: 12460 AN XY: 74374

African (AFR) AF: 0.358 AC: 14820 AN: 41436

American (AMR) AF: 0.270 AC: 4129 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1534 AN: 5186

South Asian (SAS) AF: 0.0781 AC: 377 AN: 4826

European-Finnish (FIN) AF: 0.0528 AC: 560 AN: 10600

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0501 AC: 3409 AN: 67998

Other (OTH) AF: 0.147 AC: 311 AN: 2112

Alfa AF: 0.0773 Hom.: 1711

Bravo AF: 0.195

Asia WGS AF: 0.228 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.52
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs4790953; hg19: chr17-63227030;