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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377379	XR_001741520.3	n.282+3572C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310194	ENST00000848071.1	n.228-19746G>A		intron_variant	Intron 1 of 1
ENSG00000310194	ENST00000848072.1	n.186-2847G>A		intron_variant	Intron 1 of 3
ENSG00000310194	ENST00000848073.1	n.115-19746G>A		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs7690426; hg19: chr4-115384107;