ENST00000438969.2:n.353-469G>A

Variant names:

• chr7-137345599-C-T
• rs161335
• ENST00000438969.2:n.353-469G>A

Variant summary

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

The ENST00000438969.2(ENSG00000228031):​n.353-469G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,792 control chromosomes in the GnomAD database, including 9,939 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 0.34 (9939 hom., cov: 31)
• Consequence: ENSG00000228031 ENST00000438969.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 3 publications found

Genes affected

ENSG00000228031 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228031	ENST00000438969.2	n.353-469G>A		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51074 AN: 151674 Hom.: 9935 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.336 AC: 51067 AN: 151792 Hom.: 9939 Cov.: 31 AF XY: 0.340 AC XY: 25239 AN XY: 74190

African (AFR) AF: 0.132 AC: 5462 AN: 41364

American (AMR) AF: 0.427 AC: 6515 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3468

East Asian (EAS) AF: 0.384 AC: 1971 AN: 5132

South Asian (SAS) AF: 0.326 AC: 1564 AN: 4802

European-Finnish (FIN) AF: 0.440 AC: 4633 AN: 10532

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28384 AN: 67928

Other (OTH) AF: 0.353 AC: 745 AN: 2108

Alfa AF: 0.375 Hom.: 3331

Bravo AF: 0.331

Asia WGS AF: 0.352 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.53
PhyloP100		-0.010

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs161335; hg19: chr7-137030345;