rs10511176

Variant names:

• chr3-99607657-T-C
• rs10511176
• ENST00000462011.1:n.436+9158T>C

Variant summary

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

The ENST00000462011.1(ENSG00000244464):​n.436+9158T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0747 in 152,198 control chromosomes in the GnomAD database, including 502 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 0.075 (502 hom., cov: 33)
• Consequence: ENSG00000244464 ENST00000462011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

Genes affected

ENSG00000244464 (HGNC:):

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 = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000244464	ENST00000462011.1	n.436+9158T>C		intron_variant	Intron 1 of 1	2
ENSG00000244464	ENST00000655531.1	n.395+9158T>C		intron_variant	Intron 1 of 2
ENSG00000244464	ENST00000660954.1	n.395+9158T>C		intron_variant	Intron 1 of 2
ENSG00000244464	ENST00000666141.1	n.411+9158T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0746 AC: 11344 AN: 152080 Hom.: 502 Cov.: 33

Gnomad AFR AF: 0.0973

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0923

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0495

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.0747 AC: 11363 AN: 152198 Hom.: 502 Cov.: 33 AF XY: 0.0767 AC XY: 5711 AN XY: 74414

Gnomad4 AFR AF: 0.0972

Gnomad4 AMR AF: 0.0928

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0601

Gnomad4 NFE AF: 0.0494

Gnomad4 OTH AF: 0.0943

Alfa AF: 0.0574 Hom.: 371

Bravo AF: 0.0785

Asia WGS AF: 0.163 AC: 567 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	2.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511176; hg19: chr3-99326501;