rs12610529

Variant names:

• chr19-6879532-G-T
• rs12610529

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 0.0823 in 152,176 control chromosomes in the GnomAD database, including 823 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 0.082 (823 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.277 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: 0.0824 AC: 12522 AN: 152058 Hom.: 825 Cov.: 31

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0952

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.0823 AC: 12523 AN: 152176 Hom.: 823 Cov.: 31 AF XY: 0.0879 AC XY: 6541 AN XY: 74388

African (AFR) AF: 0.0221 AC: 918 AN: 41542

American (AMR) AF: 0.135 AC: 2063 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0952 AC: 330 AN: 3468

East Asian (EAS) AF: 0.289 AC: 1494 AN: 5168

South Asian (SAS) AF: 0.0822 AC: 396 AN: 4818

European-Finnish (FIN) AF: 0.145 AC: 1531 AN: 10590

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0795 AC: 5407 AN: 67996

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.0783 Hom.: 319

Bravo AF: 0.0818

Asia WGS AF: 0.163 AC: 567 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	2.0
DANN	Benign	0.63
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs12610529; hg19: chr19-6879543;