chr10-56937456-A-C

Variant names:

• chr10-56937456-A-C
• rs12414237

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 0.107 in 152,172 control chromosomes in the GnomAD database, including 1,148 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 0.11 (1148 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 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: 0.107 AC: 16200 AN: 152054 Hom.: 1144 Cov.: 32

Gnomad AFR AF: 0.0570

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0925

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0986

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.107 AC: 16226 AN: 152172 Hom.: 1148 Cov.: 32 AF XY: 0.110 AC XY: 8199 AN XY: 74396

African (AFR) AF: 0.0570 AC: 2368 AN: 41556

American (AMR) AF: 0.190 AC: 2897 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0925 AC: 321 AN: 3472

East Asian (EAS) AF: 0.273 AC: 1412 AN: 5164

South Asian (SAS) AF: 0.219 AC: 1055 AN: 4820

European-Finnish (FIN) AF: 0.0985 AC: 1044 AN: 10602

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0985 AC: 6697 AN: 67958

Other (OTH) AF: 0.109 AC: 230 AN: 2114

Alfa AF: 0.102 Hom.: 863

Bravo AF: 0.114

Asia WGS AF: 0.199 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.92
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs12414237; hg19: chr10-58697216;