10-71007652-T-C

Position:

• chr10-71007652-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 0.0984 in 152,178 control chromosomes in the GnomAD database, including 788 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 0.098 (788 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.71007652T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285300	ENST00000646051.1	n.259-18927T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0983 AC: 14948 AN: 152060 Hom.: 785 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0777

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.0984 AC: 14975 AN: 152178 Hom.: 788 Cov.: 33 AF XY: 0.0971 AC XY: 7226 AN XY: 74414

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0776

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.0903

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.0878 Hom.: 837

Bravo AF: 0.103

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509328; hg19: chr10-72767409;