rs7515001

Variant names:

• chr1-171387616-A-G
• rs7515001

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 0.296 in 152,032 control chromosomes in the GnomAD database, including 6,778 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 0.30 (6778 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 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: 0.296 AC: 44953 AN: 151912 Hom.: 6773 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.296 AC: 44991 AN: 152032 Hom.: 6778 Cov.: 32 AF XY: 0.298 AC XY: 22134 AN XY: 74324

African (AFR) AF: 0.285 AC: 11822 AN: 41466

American (AMR) AF: 0.298 AC: 4548 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1094 AN: 3472

East Asian (EAS) AF: 0.434 AC: 2235 AN: 5150

South Asian (SAS) AF: 0.402 AC: 1939 AN: 4822

European-Finnish (FIN) AF: 0.258 AC: 2725 AN: 10574

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19764 AN: 67964

Other (OTH) AF: 0.306 AC: 646 AN: 2112

Alfa AF: 0.297 Hom.: 28945

Bravo AF: 0.297

Asia WGS AF: 0.378 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.8
DANN	Benign	0.86
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs7515001; hg19: chr1-171356755;