ENST00000674692.1:n.1247+345T>C

Variant names:

• chr2-190759747-A-G
• rs1263100
• ENST00000674692.1:n.1247+345T>C

Variant summary

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

The ENST00000674692.1(ENSG00000228509):​n.1247+345T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,808 control chromosomes in the GnomAD database, including 12,147 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 0.39 (12147 hom., cov: 30)
• Consequence: ENSG00000228509 ENST00000674692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 3 publications found

Genes affected

ENSG00000228509 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907946	XR_007087780.1	n.410+345T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228509	ENST00000674692.1	n.1247+345T>C		intron_variant	Intron 1 of 1
ENSG00000228509	ENST00000676095.2	n.195-20416T>C		intron_variant	Intron 2 of 8
ENSG00000228509	ENST00000676284.2	n.410+345T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59216 AN: 151690 Hom.: 12144 Cov.: 30

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.390 AC: 59234 AN: 151808 Hom.: 12147 Cov.: 30 AF XY: 0.381 AC XY: 28257 AN XY: 74210

African (AFR) AF: 0.305 AC: 12621 AN: 41358

American (AMR) AF: 0.324 AC: 4948 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1637 AN: 3468

East Asian (EAS) AF: 0.311 AC: 1604 AN: 5154

South Asian (SAS) AF: 0.229 AC: 1100 AN: 4814

European-Finnish (FIN) AF: 0.365 AC: 3842 AN: 10526

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 31960 AN: 67920

Other (OTH) AF: 0.396 AC: 835 AN: 2108

Alfa AF: 0.413 Hom.: 2232

Bravo AF: 0.387

Asia WGS AF: 0.286 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.75
DANN	Benign	0.68
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1263100; hg19: chr2-191624473;