rs7513590

Variant names:

• chr1-5110652-A-G
• rs7513590

Your query was ambiguous. Multiple possible variants found:

• chr1-5110652-A-G
• chr1-5110652-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 0.145 in 152,270 control chromosomes in the GnomAD database, including 1,892 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 0.14 (1892 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 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: 0.145 AC: 21999 AN: 152152 Hom.: 1880 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.0902

Gnomad EAS AF: 0.0732

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.145 AC: 22056 AN: 152270 Hom.: 1892 Cov.: 33 AF XY: 0.143 AC XY: 10638 AN XY: 74458

African (AFR) AF: 0.242 AC: 10062 AN: 41540

American (AMR) AF: 0.174 AC: 2667 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0902 AC: 313 AN: 3470

East Asian (EAS) AF: 0.0730 AC: 378 AN: 5180

South Asian (SAS) AF: 0.0905 AC: 437 AN: 4828

European-Finnish (FIN) AF: 0.0818 AC: 869 AN: 10618

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6973 AN: 68020

Other (OTH) AF: 0.117 AC: 247 AN: 2112

Alfa AF: 0.116 Hom.: 5035

Bravo AF: 0.157

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.68
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs7513590; hg19: chr1-5170712;