7-94248975-G-T

Variant names:

• chr7-94248975-G-T
• rs949524
• ENST00000834100.1:n.365-14749C>A

Variant summary

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

The ENST00000834100.1(ENSG00000285090):​n.365-14749C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,036 control chromosomes in the GnomAD database, including 5,539 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 0.17 (5539 hom., cov: 32)
• Consequence: ENSG00000285090 ENST00000834100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.617
• Publications: 1 publications found

Genes affected

ENSG00000285090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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
ENSG00000285090	ENST00000834100.1	n.365-14749C>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25773 AN: 151918 Hom.: 5508 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0680

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0234

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.170 AC: 25857 AN: 152036 Hom.: 5539 Cov.: 32 AF XY: 0.166 AC XY: 12329 AN XY: 74338

African (AFR) AF: 0.503 AC: 20832 AN: 41384

American (AMR) AF: 0.120 AC: 1827 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3472

East Asian (EAS) AF: 0.116 AC: 600 AN: 5170

South Asian (SAS) AF: 0.0685 AC: 330 AN: 4820

European-Finnish (FIN) AF: 0.0216 AC: 229 AN: 10582

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0234 AC: 1593 AN: 68020

Other (OTH) AF: 0.137 AC: 290 AN: 2112

Alfa AF: 0.0741 Hom.: 2101

Bravo AF: 0.192

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.60
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs949524; hg19: chr7-93878287;