rs1337987

chr10-111778430-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.343

Alfa AF: 0.303 Hom.: 7905

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1337987; hg19: chr10-113538188;