chr10-111778430-C-T

Variant names:

• chr10-111778430-C-T
• rs1337987

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 0.323 in 151,994 control chromosomes in the GnomAD database, including 8,216 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 0.32 (8216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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: 0.323 AC: 49069 AN: 151880 Hom.: 8197 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.323 AC: 49137 AN: 151994 Hom.: 8216 Cov.: 32 AF XY: 0.323 AC XY: 23994 AN XY: 74286

African (AFR) AF: 0.344 AC: 14251 AN: 41444

American (AMR) AF: 0.398 AC: 6082 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1028 AN: 3466

East Asian (EAS) AF: 0.479 AC: 2460 AN: 5140

South Asian (SAS) AF: 0.264 AC: 1267 AN: 4808

European-Finnish (FIN) AF: 0.257 AC: 2724 AN: 10582

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20159 AN: 67972

Other (OTH) AF: 0.343 AC: 724 AN: 2108

Alfa AF: 0.306 Hom.: 10089

Bravo AF: 0.339

Asia WGS AF: 0.390 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.48
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1337987; hg19: chr10-113538188;