rs10412302

Variant names:

• chr19-56886142-T-C
• rs10412302

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 0.328 in 152,044 control chromosomes in the GnomAD database, including 8,394 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 0.33 (8394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49867 AN: 151926 Hom.: 8382 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.328 AC: 49921 AN: 152044 Hom.: 8394 Cov.: 32 AF XY: 0.325 AC XY: 24131 AN XY: 74320

African (AFR) AF: 0.364 AC: 15119 AN: 41482

American (AMR) AF: 0.349 AC: 5333 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1183 AN: 3464

East Asian (EAS) AF: 0.179 AC: 924 AN: 5166

South Asian (SAS) AF: 0.260 AC: 1254 AN: 4818

European-Finnish (FIN) AF: 0.305 AC: 3235 AN: 10592

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21788 AN: 67942

Other (OTH) AF: 0.344 AC: 724 AN: 2104

Alfa AF: 0.329 Hom.: 2874

Bravo AF: 0.334

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.67
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10412302; hg19: chr19-57397510;