chr19-10870676-A-G

Variant names:

• chr19-10870676-A-G
• rs12460421

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 0.423 in 151,976 control chromosomes in the GnomAD database, including 13,650 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 0.42 (13650 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.16).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 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: 0.423 AC: 64205 AN: 151858 Hom.: 13604 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.423 AC: 64307 AN: 151976 Hom.: 13650 Cov.: 31 AF XY: 0.425 AC XY: 31551 AN XY: 74290

African (AFR) AF: 0.424 AC: 17577 AN: 41456

American (AMR) AF: 0.364 AC: 5569 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1500 AN: 3472

East Asian (EAS) AF: 0.567 AC: 2919 AN: 5150

South Asian (SAS) AF: 0.437 AC: 2104 AN: 4816

European-Finnish (FIN) AF: 0.458 AC: 4832 AN: 10550

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28415 AN: 67936

Other (OTH) AF: 0.418 AC: 882 AN: 2110

Alfa AF: 0.416 Hom.: 26556

Bravo AF: 0.418

Asia WGS AF: 0.480 AC: 1669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.13
DANN	Benign	0.16
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs12460421; hg19: chr19-10981352;