7-109363517-C-T

Variant names:

• chr7-109363517-C-T
• rs10277209
• ENST00000736541.1:n.295+667G>A

Variant summary

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

The ENST00000736541.1(ENSG00000230941):​n.295+667G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 151,834 control chromosomes in the GnomAD database, including 51,460 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 0.81 (51460 hom., cov: 31)
• Consequence: ENSG00000230941 ENST00000736541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 9 publications found

Genes affected

ENSG00000230941 (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 (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736541.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230941	ENST00000736541.1		n.295+667G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123629 AN: 151716 Hom.: 51444 Cov.: 31

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.815 AC: 123692 AN: 151834 Hom.: 51460 Cov.: 31 AF XY: 0.819 AC XY: 60780 AN XY: 74202

African (AFR) AF: 0.626 AC: 25909 AN: 41394

American (AMR) AF: 0.877 AC: 13315 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2982 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5132 AN: 5152

South Asian (SAS) AF: 0.950 AC: 4579 AN: 4818

European-Finnish (FIN) AF: 0.862 AC: 9101 AN: 10562

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59900 AN: 67948

Other (OTH) AF: 0.820 AC: 1721 AN: 2100

Alfa AF: 0.855 Hom.: 21356

Bravo AF: 0.805

Asia WGS AF: 0.928 AC: 3224 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.7
DANN	Benign	0.51
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10277209; hg19: chr7-109003574;