ENST00000796634.1:n.109+11605C>T

Variant names:

• chr6-157340053-C-T
• rs4708937
• ENST00000796634.1:n.109+11605C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000796634.1(ENSG00000303704):​n.109+11605C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,818 control chromosomes in the GnomAD database, including 10,047 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 0.35 (10047 hom., cov: 32)
• Consequence: ENSG00000303704 ENST00000796634.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 1 publications found

Genes affected

ENSG00000303704 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 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
ENSG00000303704	ENST00000796634.1	n.109+11605C>T		intron_variant	Intron 1 of 2
ENSG00000303704	ENST00000796635.1	n.245+7602C>T		intron_variant	Intron 2 of 3
ENSG00000303704	ENST00000796636.1	n.265+7602C>T		intron_variant	Intron 2 of 3
ENSG00000303704	ENST00000796637.1	n.392+7602C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53603 AN: 151700 Hom.: 10017 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.354 AC: 53698 AN: 151818 Hom.: 10047 Cov.: 32 AF XY: 0.355 AC XY: 26370 AN XY: 74180

African (AFR) AF: 0.461 AC: 19075 AN: 41374

American (AMR) AF: 0.406 AC: 6191 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3470

East Asian (EAS) AF: 0.562 AC: 2892 AN: 5148

South Asian (SAS) AF: 0.328 AC: 1575 AN: 4802

European-Finnish (FIN) AF: 0.302 AC: 3178 AN: 10520

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 18988 AN: 67932

Other (OTH) AF: 0.351 AC: 741 AN: 2114

Alfa AF: 0.227 Hom.: 821

Bravo AF: 0.370

Asia WGS AF: 0.441 AC: 1531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
DANN	Benign	0.57
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4708937; hg19: chr6-157761085; COSMIC: COSV56940821;