rs10886971

chr10-83714375-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659573.1(ENSG00000286876):n.200-3500G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,074 control chromosomes in the GnomAD database, including 1,393 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 0.10 (1393 hom., cov: 33)
• Consequence: ENST00000659573.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

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 = 0.484 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
	ENST00000659573.1	n.200-3500G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15666 AN: 151956 Hom.: 1392 Cov.: 33

Gnomad AFR AF: 0.0243

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.103 AC: 15650 AN: 152074 Hom.: 1393 Cov.: 33 AF XY: 0.110 AC XY: 8167 AN XY: 74340

Gnomad4 AFR AF: 0.0243

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0900 Hom.: 78

Bravo AF: 0.100

Asia WGS AF: 0.278 AC: 964 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.5
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10886971; hg19: chr10-85474131;