chr7-86011096-A-G

Variant names:

• chr7-86011096-A-G
• rs13236080
• ENST00000757672.1:n.224-44495T>C

Variant summary

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

The ENST00000757672.1(ENSG00000298738):​n.224-44495T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,130 control chromosomes in the GnomAD database, including 2,365 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 0.15 (2365 hom., cov: 32)
• Consequence: ENSG00000298738 ENST00000757672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 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	ENST00000757672.1	n.224-44495T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22506 AN: 152012 Hom.: 2355 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0655

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0248

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.148 AC: 22548 AN: 152130 Hom.: 2365 Cov.: 32 AF XY: 0.145 AC XY: 10803 AN XY: 74382

African (AFR) AF: 0.291 AC: 12076 AN: 41470

American (AMR) AF: 0.0653 AC: 999 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0700 AC: 243 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0251 AC: 121 AN: 4830

European-Finnish (FIN) AF: 0.147 AC: 1555 AN: 10584

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7194 AN: 67992

Other (OTH) AF: 0.116 AC: 245 AN: 2110

Alfa AF: 0.110 Hom.: 642

Bravo AF: 0.150

Asia WGS AF: 0.0270 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.070
DANN	Benign	0.54
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs13236080; hg19: chr7-85640412;