7-85960922-T-G

Variant names:

• chr7-85960922-T-G
• rs10275700
• ENST00000757675.1:n.68+5613A>C

Variant summary

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

The ENST00000757675.1(ENSG00000298738):​n.68+5613A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,856 control chromosomes in the GnomAD database, including 29,344 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 0.60 (29344 hom., cov: 30)
• Consequence: ENSG00000298738 ENST00000757675.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 2 publications found

Genes affected

ENSG00000298738 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 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
ENSG00000298738	ENST00000757675.1	n.68+5613A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91007 AN: 151738 Hom.: 29287 Cov.: 30

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.600 AC: 91119 AN: 151856 Hom.: 29344 Cov.: 30 AF XY: 0.594 AC XY: 44045 AN XY: 74198

African (AFR) AF: 0.848 AC: 35138 AN: 41436

American (AMR) AF: 0.490 AC: 7461 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1900 AN: 3468

East Asian (EAS) AF: 0.425 AC: 2188 AN: 5144

South Asian (SAS) AF: 0.423 AC: 2035 AN: 4812

European-Finnish (FIN) AF: 0.523 AC: 5509 AN: 10528

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34791 AN: 67928

Other (OTH) AF: 0.586 AC: 1230 AN: 2100

Alfa AF: 0.510 Hom.: 5060

Bravo AF: 0.612

Asia WGS AF: 0.462 AC: 1606 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.48
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs10275700; hg19: chr7-85590238;