10-114981742-C-G

Variant names:

• chr10-114981742-C-G
• rs12772737

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 0.223 in 152,146 control chromosomes in the GnomAD database, including 4,487 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 0.22 (4487 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.312 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: 0.223 AC: 33904 AN: 152028 Hom.: 4484 Cov.: 31

Gnomad AFR AF: 0.0958

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.223 AC: 33909 AN: 152146 Hom.: 4487 Cov.: 31 AF XY: 0.219 AC XY: 16278 AN XY: 74378

African (AFR) AF: 0.0956 AC: 3970 AN: 41524

American (AMR) AF: 0.171 AC: 2617 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3472

East Asian (EAS) AF: 0.0315 AC: 163 AN: 5178

South Asian (SAS) AF: 0.301 AC: 1453 AN: 4826

European-Finnish (FIN) AF: 0.239 AC: 2534 AN: 10582

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21474 AN: 67962

Other (OTH) AF: 0.227 AC: 480 AN: 2114

Alfa AF: 0.157 Hom.: 329

Bravo AF: 0.208

Asia WGS AF: 0.193 AC: 671 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	0.17
DANN	Benign	0.60
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs12772737; hg19: chr10-116741501;