10-37276059-T-C

Position:

• chr10-37276059-T-C

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 0.548 in 152,078 control chromosomes in the GnomAD database, including 23,298 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 0.55 (23298 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37276059T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00993	ENST00000420453.1	n.350+11422T>C		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83203 AN: 151958 Hom.: 23254 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.548 AC: 83302 AN: 152078 Hom.: 23298 Cov.: 32 AF XY: 0.553 AC XY: 41144 AN XY: 74336

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.534

Alfa AF: 0.521 Hom.: 10276

Bravo AF: 0.544

Asia WGS AF: 0.716 AC: 2488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1200826; hg19: chr10-37564987;