chr7-101601694-C-A

Variant names:

• chr7-101601694-C-A
• rs17135662
• ENST00000786892.1:n.168+497G>T

Variant summary

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

The ENST00000786892.1(ENSG00000302449):​n.168+497G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 151,934 control chromosomes in the GnomAD database, including 2,215 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 (2215 hom., cov: 33)
• Consequence: ENSG00000302449 ENST00000786892.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 4 publications found

Genes affected

ENSG00000302449 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.188 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
ENSG00000302449	ENST00000786892.1	n.168+497G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25655 AN: 151816 Hom.: 2205 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.169 AC: 25682 AN: 151934 Hom.: 2215 Cov.: 33 AF XY: 0.166 AC XY: 12337 AN XY: 74274

African (AFR) AF: 0.139 AC: 5761 AN: 41378

American (AMR) AF: 0.144 AC: 2194 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3470

East Asian (EAS) AF: 0.158 AC: 815 AN: 5160

South Asian (SAS) AF: 0.194 AC: 934 AN: 4806

European-Finnish (FIN) AF: 0.177 AC: 1871 AN: 10572

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.191 AC: 12991 AN: 67956

Other (OTH) AF: 0.179 AC: 378 AN: 2110

Alfa AF: 0.185 Hom.: 2083

Bravo AF: 0.167

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.66
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs17135662; hg19: chr7-101244974; COSMIC: COSV53499558;