rs11767787

Variant names:

• chr7-95397441-T-C
• rs11767787
• ENST00000702974.1:n.945T>C

Variant summary

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

The ENST00000702974.1(ENSG00000233942):​n.945T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,534 control chromosomes in the GnomAD database, including 6,805 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 0.29 (6805 hom., cov: 30)
• Consequence: ENSG00000233942 ENST00000702974.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 6 publications found

Genes affected

ENSG00000233942 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702974.1. 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
	ENSG00000233942	ENST00000702974.1		n.945T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000233942	ENST00000718462.1		n.589+413T>C		intron	N/A
	ENSG00000233942	ENST00000718463.1		n.572+413T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43941 AN: 151416 Hom.: 6790 Cov.: 30

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.290 AC: 43979 AN: 151534 Hom.: 6805 Cov.: 30 AF XY: 0.298 AC XY: 22088 AN XY: 74034

African (AFR) AF: 0.317 AC: 13070 AN: 41254

American (AMR) AF: 0.232 AC: 3541 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 667 AN: 3466

East Asian (EAS) AF: 0.172 AC: 881 AN: 5110

South Asian (SAS) AF: 0.382 AC: 1832 AN: 4796

European-Finnish (FIN) AF: 0.464 AC: 4854 AN: 10468

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18086 AN: 67906

Other (OTH) AF: 0.259 AC: 543 AN: 2096

Alfa AF: 0.292 Hom.: 828

Bravo AF: 0.269

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.57
PhyloP100		0.23

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: rs11767787;

hg19: chr7-95026753;