rs12565497

Variant names:

• chr1-110979183-G-A
• rs12565497

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 0.267 in 149,404 control chromosomes in the GnomAD database, including 6,153 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 0.27 (6153 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 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: 0.267 AC: 39809 AN: 149292 Hom.: 6145 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.267 AC: 39829 AN: 149404 Hom.: 6153 Cov.: 31 AF XY: 0.266 AC XY: 19437 AN XY: 73038

African (AFR) AF: 0.164 AC: 6402 AN: 39008

American (AMR) AF: 0.321 AC: 4877 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 855 AN: 3470

East Asian (EAS) AF: 0.342 AC: 1767 AN: 5168

South Asian (SAS) AF: 0.201 AC: 970 AN: 4818

European-Finnish (FIN) AF: 0.306 AC: 3218 AN: 10524

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.308 AC: 20905 AN: 67934

Other (OTH) AF: 0.256 AC: 534 AN: 2086

Alfa AF: 0.269 Hom.: 881

Bravo AF: 0.261

Asia WGS AF: 0.205 AC: 709 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.56
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs12565497; hg19: chr1-111521805;