chr3-99607657-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000244464 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.0972 AC: 4037 AN: 41524

American (AMR) AF: 0.0928 AC: 1418 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3470

East Asian (EAS) AF: 0.152 AC: 786 AN: 5176

South Asian (SAS) AF: 0.113 AC: 545 AN: 4830

European-Finnish (FIN) AF: 0.0601 AC: 638 AN: 10610

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0494 AC: 3362 AN: 67992

Other (OTH) AF: 0.0943 AC: 199 AN: 2110

Alfa AF: 0.0595 Hom.: 498

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10511176; hg19: chr3-99326501;