ENST00000716631.1:n.56+1197T>C

Variant names:

• chr6-40928917-A-G
• rs2395760
• ENST00000716631.1:n.56+1197T>C

Variant summary

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

The ENST00000716631.1(ENSG00000293636):​n.56+1197T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 152,126 control chromosomes in the GnomAD database, including 54,674 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 0.85 (54674 hom., cov: 32)
• Consequence: ENSG00000293636 ENST00000716631.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341
• Publications: 5 publications found

Genes affected

ENSG00000293636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929555	NR_110873.1	n.136-26219T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293636	ENST00000716631.1	n.56+1197T>C		intron_variant	Intron 1 of 8
ENSG00000293636	ENST00000716633.1	n.375-26219T>C		intron_variant	Intron 3 of 7
ENSG00000293636	ENST00000740548.1	n.126-26219T>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128644 AN: 152008 Hom.: 54661 Cov.: 32

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.846 AC: 128705 AN: 152126 Hom.: 54674 Cov.: 32 AF XY: 0.845 AC XY: 62873 AN XY: 74364

African (AFR) AF: 0.758 AC: 31436 AN: 41450

American (AMR) AF: 0.856 AC: 13085 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2760 AN: 3472

East Asian (EAS) AF: 0.889 AC: 4595 AN: 5170

South Asian (SAS) AF: 0.848 AC: 4086 AN: 4820

European-Finnish (FIN) AF: 0.850 AC: 9001 AN: 10594

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60930 AN: 68014

Other (OTH) AF: 0.857 AC: 1811 AN: 2114

Alfa AF: 0.880 Hom.: 100827

Bravo AF: 0.843

Asia WGS AF: 0.811 AC: 2822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.75
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2395760; hg19: chr6-40896656;