rs10511713

chr9-23116601-A-G

Variant summary

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

The ENST00000640003.1(ENSG00000284418):n.251-110404T>C 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 0.0145 in 152,164 control chromosomes in the GnomAD database, including 63 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 0.014 (63 hom., cov: 32)
• Consequence: ENST00000640003.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0607 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
	ENST00000640003.1	n.251-110404T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000664493.1	n.222-110404T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0145 AC: 2202 AN: 152046 Hom.: 63 Cov.: 32

Gnomad AFR AF: 0.00762

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0513

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.0665

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.00857

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00505

Gnomad OTH AF: 0.0125

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

GnomAD4 genome AF: 0.0145 AC: 2200 AN: 152164 Hom.: 63 Cov.: 32 AF XY: 0.0163 AC XY: 1213 AN XY: 74386

Gnomad4 AFR AF: 0.00762

Gnomad4 AMR AF: 0.0512

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.0664

Gnomad4 SAS AF: 0.0612

Gnomad4 FIN AF: 0.00857

Gnomad4 NFE AF: 0.00505

Gnomad4 OTH AF: 0.0123

Alfa AF: 0.0112 Hom.: 5

Bravo AF: 0.0160

Asia WGS AF: 0.0680 AC: 236 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	8.9
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511713; hg19: chr9-23116600;