rs1575013

Variant names:

• chr7-113088855-G-A
• rs1575013

Your query was ambiguous. Multiple possible variants found:

• chr7-113088855-G-A
• chr7-113088855-G-C

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 0.29 in 151,918 control chromosomes in the GnomAD database, including 7,923 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 0.29 (7923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• 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 (AFR) allele frequency at 95% confidence interval = 0.498 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: 0.290 AC: 43947 AN: 151798 Hom.: 7908 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0516

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.290 AC: 43992 AN: 151918 Hom.: 7923 Cov.: 32 AF XY: 0.286 AC XY: 21231 AN XY: 74252

African (AFR) AF: 0.504 AC: 20875 AN: 41414

American (AMR) AF: 0.181 AC: 2764 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 904 AN: 3464

East Asian (EAS) AF: 0.0520 AC: 269 AN: 5178

South Asian (SAS) AF: 0.370 AC: 1782 AN: 4820

European-Finnish (FIN) AF: 0.156 AC: 1647 AN: 10538

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.219 AC: 14868 AN: 67918

Other (OTH) AF: 0.285 AC: 602 AN: 2110

Alfa AF: 0.218 Hom.: 1990

Bravo AF: 0.296

Asia WGS AF: 0.207 AC: 720 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.35
DANN	Benign	0.26
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1575013; hg19: chr7-112728910;