chr7-26086909-G-A

Variant names:

• chr7-26086909-G-A
• rs10233157
• ENST00000718758.1:n.219-17108C>T

Variant summary

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

The ENST00000718758.1(ENSG00000293754):​n.219-17108C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 151,202 control chromosomes in the GnomAD database, including 2,267 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 0.11 (2267 hom., cov: 32)
• Consequence: ENSG00000293754 ENST00000718758.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 1 publications found

Genes affected

ENSG00000293754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718758.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293754	ENST00000718758.1		n.219-17108C>T		intron	N/A
	ENSG00000293754	ENST00000718759.1		n.207-17108C>T		intron	N/A
	ENSG00000293754	ENST00000718760.1		n.190-17108C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16251 AN: 151084 Hom.: 2266 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.0259

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.00851

Gnomad OTH AF: 0.0857

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

GnomAD4 genome AF: 0.108 AC: 16277 AN: 151202 Hom.: 2267 Cov.: 32 AF XY: 0.107 AC XY: 7923 AN XY: 73804

African (AFR) AF: 0.304 AC: 12518 AN: 41154

American (AMR) AF: 0.0424 AC: 644 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.0231 AC: 80 AN: 3458

East Asian (EAS) AF: 0.311 AC: 1597 AN: 5136

South Asian (SAS) AF: 0.0831 AC: 397 AN: 4776

European-Finnish (FIN) AF: 0.0259 AC: 268 AN: 10360

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.00851 AC: 577 AN: 67830

Other (OTH) AF: 0.0852 AC: 179 AN: 2100

Alfa AF: 0.0390 Hom.: 313

Bravo AF: 0.120

Asia WGS AF: 0.163 AC: 568 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.19
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10233157; hg19: chr7-26126529;