7-76713262-C-G

Variant names:

• chr7-76713262-C-G
• rs10488497
• ENST00000740833.1:n.406+15204G>C

Variant summary

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

The ENST00000740833.1(ENSG00000296620):​n.406+15204G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,964 control chromosomes in the GnomAD database, including 4,213 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 0.23 (4213 hom., cov: 31)
• Consequence: ENSG00000296620 ENST00000740833.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 6 publications found

Genes affected

ENSG00000296620 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 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
ENSG00000296620	ENST00000740833.1	n.406+15204G>C		intron_variant	Intron 1 of 2
ENSG00000296620	ENST00000740834.1	n.515+15204G>C		intron_variant	Intron 1 of 3
ENSG00000296620	ENST00000740835.1	n.202+15482G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34297 AN: 151846 Hom.: 4209 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0168

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.226 AC: 34322 AN: 151964 Hom.: 4213 Cov.: 31 AF XY: 0.226 AC XY: 16755 AN XY: 74258

African (AFR) AF: 0.137 AC: 5684 AN: 41418

American (AMR) AF: 0.268 AC: 4088 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1029 AN: 3466

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5174

South Asian (SAS) AF: 0.243 AC: 1171 AN: 4812

European-Finnish (FIN) AF: 0.233 AC: 2455 AN: 10552

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18893 AN: 67970

Other (OTH) AF: 0.251 AC: 528 AN: 2102

Alfa AF: 0.0865 Hom.: 147

Bravo AF: 0.222

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10488497; hg19: chr7-76342579;