rs11768389

Variant names:

• chr7-127510196-T-C
• rs11768389
• ENST00000731796.1:n.70-4830A>G

Variant summary

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

The ENST00000731796.1(ENSG00000295686):​n.70-4830A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,136 control chromosomes in the GnomAD database, including 7,057 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 0.27 (7057 hom., cov: 31)
• Consequence: ENSG00000295686 ENST00000731796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 5 publications found

Genes affected

ENSG00000295686 (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 = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731796.1. 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
	ENSG00000295686	ENST00000731796.1		n.70-4830A>G		intron	N/A
	ENSG00000295686	ENST00000731797.1		n.355-24914A>G		intron	N/A
	ENSG00000295686	ENST00000731798.1		n.244-4830A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40461 AN: 151038 Hom.: 7053 Cov.: 31

Gnomad AFR AF: 0.0658

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.268 AC: 40463 AN: 151136 Hom.: 7057 Cov.: 31 AF XY: 0.276 AC XY: 20375 AN XY: 73818

African (AFR) AF: 0.0657 AC: 2702 AN: 41148

American (AMR) AF: 0.298 AC: 4525 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3458

East Asian (EAS) AF: 0.653 AC: 3357 AN: 5142

South Asian (SAS) AF: 0.315 AC: 1504 AN: 4778

European-Finnish (FIN) AF: 0.425 AC: 4386 AN: 10318

Middle Eastern (MID) AF: 0.130 AC: 37 AN: 284

European-Non Finnish (NFE) AF: 0.330 AC: 22380 AN: 67814

Other (OTH) AF: 0.260 AC: 547 AN: 2102

Alfa AF: 0.277 Hom.: 1825

Bravo AF: 0.251

Asia WGS AF: 0.437 AC: 1516 AN: 3478

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	0.75
PhyloP100		0.29

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: rs11768389;

hg19: chr7-127150250;