7-118781541-C-T

Variant names:

• chr7-118781541-C-T
• rs2250260
• ENST00000761310.1:n.151-16968G>A

Variant summary

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

The ENST00000761310.1(ENSG00000299159):​n.151-16968G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 151,908 control chromosomes in the GnomAD database, including 2,578 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 (2578 hom., cov: 32)
• Consequence: ENSG00000299159 ENST00000761310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 1 publications found

Genes affected

ENSG00000299159 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761310.1. 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
	ENSG00000299159	ENST00000761310.1		n.151-16968G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16074 AN: 151790 Hom.: 2567 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0446

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0216

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00975

Gnomad OTH AF: 0.0790

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

GnomAD4 genome AF: 0.106 AC: 16118 AN: 151908 Hom.: 2578 Cov.: 32 AF XY: 0.102 AC XY: 7588 AN XY: 74240

African (AFR) AF: 0.347 AC: 14362 AN: 41398

American (AMR) AF: 0.0445 AC: 677 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.00865 AC: 30 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5164

South Asian (SAS) AF: 0.0222 AC: 107 AN: 4820

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10592

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00973 AC: 661 AN: 67922

Other (OTH) AF: 0.0782 AC: 165 AN: 2110

Alfa AF: 0.0313 Hom.: 90

Bravo AF: 0.118

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.71
PhyloP100		-0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2250260;

hg19: chr7-118421595;