rs7690426

Variant names:

• chr4-114462951-C-T
• rs7690426
• ENST00000848071.1:n.228-19746G>A

Variant summary

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

The ENST00000848071.1(ENSG00000310194):​n.228-19746G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,024 control chromosomes in the GnomAD database, including 14,686 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 0.41 (14686 hom., cov: 33)
• Consequence: ENSG00000310194 ENST00000848071.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 6 publications found

Genes affected

ENSG00000310194 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848071.1. 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
	ENSG00000310194	ENST00000848071.1		n.228-19746G>A		intron	N/A
	ENSG00000310194	ENST00000848072.1		n.186-2847G>A		intron	N/A
	ENSG00000310194	ENST00000848073.1		n.115-19746G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62261 AN: 151904 Hom.: 14692 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.409 AC: 62241 AN: 152024 Hom.: 14686 Cov.: 33 AF XY: 0.408 AC XY: 30351 AN XY: 74302

African (AFR) AF: 0.152 AC: 6304 AN: 41508

American (AMR) AF: 0.474 AC: 7239 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1857 AN: 3468

East Asian (EAS) AF: 0.438 AC: 2263 AN: 5172

South Asian (SAS) AF: 0.537 AC: 2593 AN: 4826

European-Finnish (FIN) AF: 0.423 AC: 4459 AN: 10552

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 35996 AN: 67922

Other (OTH) AF: 0.420 AC: 887 AN: 2112

Alfa AF: 0.466 Hom.: 8291

Bravo AF: 0.399

Asia WGS AF: 0.471 AC: 1633 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.44
PhyloP100		-0.21

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: rs7690426;

hg19: chr4-115384107;