chr7-70898797-G-T

Variant names:

• chr7-70898797-G-T
• rs10277450
• ENST00000760408.1:n.106+4070G>T

Variant summary

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

The ENST00000760408.1(ENSG00000299089):​n.106+4070G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,506 control chromosomes in the GnomAD database, including 13,029 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 0.40 (13029 hom., cov: 30)
• Consequence: ENSG00000299089 ENST00000760408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434
• Publications: 2 publications found

Genes affected

ENSG00000299089 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 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
ENSG00000299089	ENST00000760408.1	n.106+4070G>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60000 AN: 151386 Hom.: 13021 Cov.: 30

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.396 AC: 60025 AN: 151506 Hom.: 13029 Cov.: 30 AF XY: 0.404 AC XY: 29865 AN XY: 74002

African (AFR) AF: 0.218 AC: 8978 AN: 41248

American (AMR) AF: 0.436 AC: 6632 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1258 AN: 3468

East Asian (EAS) AF: 0.507 AC: 2605 AN: 5136

South Asian (SAS) AF: 0.430 AC: 2059 AN: 4792

European-Finnish (FIN) AF: 0.612 AC: 6415 AN: 10482

Middle Eastern (MID) AF: 0.271 AC: 78 AN: 288

European-Non Finnish (NFE) AF: 0.452 AC: 30714 AN: 67886

Other (OTH) AF: 0.399 AC: 840 AN: 2106

Alfa AF: 0.428 Hom.: 7276

Bravo AF: 0.380

Asia WGS AF: 0.407 AC: 1415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.15
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs10277450; hg19: chr7-70363783;