rs7536585

Variant names:

• chr1-209568601-T-C
• rs7536585

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 0.165 in 152,102 control chromosomes in the GnomAD database, including 2,222 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 0.16 (2222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 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: 0.165 AC: 25035 AN: 151982 Hom.: 2222 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0465

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.165 AC: 25046 AN: 152102 Hom.: 2222 Cov.: 32 AF XY: 0.165 AC XY: 12255 AN XY: 74368

African (AFR) AF: 0.129 AC: 5353 AN: 41482

American (AMR) AF: 0.141 AC: 2147 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3470

East Asian (EAS) AF: 0.0464 AC: 241 AN: 5190

South Asian (SAS) AF: 0.194 AC: 934 AN: 4820

European-Finnish (FIN) AF: 0.189 AC: 1996 AN: 10572

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13289 AN: 67972

Other (OTH) AF: 0.164 AC: 347 AN: 2110

Alfa AF: 0.182 Hom.: 2482

Bravo AF: 0.156

Asia WGS AF: 0.114 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.47
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs7536585; hg19: chr1-209741946;