7-131603090-C-T

Variant names:

• chr7-131603090-C-T
• rs1862083
• ENST00000820764.1:n.457-12316C>T

Variant summary

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

The ENST00000820764.1(ENSG00000306749):​n.457-12316C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,914 control chromosomes in the GnomAD database, including 12,050 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 0.37 (12050 hom., cov: 32)
• Consequence: ENSG00000306749 ENST00000820764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.826
• Publications: 3 publications found

Genes affected

ENSG00000306749 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820764.1. 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
	ENSG00000306749	ENST00000820764.1		n.457-12316C>T		intron	N/A
	ENSG00000306749	ENST00000820765.1		n.435-12316C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56701 AN: 151796 Hom.: 12053 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.373 AC: 56708 AN: 151914 Hom.: 12050 Cov.: 32 AF XY: 0.376 AC XY: 27943 AN XY: 74230

African (AFR) AF: 0.159 AC: 6569 AN: 41442

American (AMR) AF: 0.347 AC: 5301 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3468

East Asian (EAS) AF: 0.424 AC: 2191 AN: 5162

South Asian (SAS) AF: 0.444 AC: 2132 AN: 4802

European-Finnish (FIN) AF: 0.535 AC: 5636 AN: 10528

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32041 AN: 67934

Other (OTH) AF: 0.380 AC: 800 AN: 2108

Alfa AF: 0.424 Hom.: 17690

Bravo AF: 0.349

Asia WGS AF: 0.421 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.85
DANN	Benign	0.39
PhyloP100		-0.83

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: rs1862083;

hg19: chr7-131287849;