2-190868631-A-T

Variant names:

• chr2-190868631-A-T
• rs7578618
• ENST00000772372.1:n.147-572T>A

Variant summary

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

The ENST00000772372.1(ENSG00000228509):​n.147-572T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,076 control chromosomes in the GnomAD database, including 16,421 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 0.44 (16421 hom., cov: 32)
• Consequence: ENSG00000228509 ENST00000772372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• 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=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 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
ENSG00000228509	ENST00000772372.1	n.147-572T>A		intron_variant	Intron 2 of 4
ENSG00000228509	ENST00000772376.1	n.162-6625T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66321 AN: 151958 Hom.: 16390 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.437 AC: 66402 AN: 152076 Hom.: 16421 Cov.: 32 AF XY: 0.432 AC XY: 32157 AN XY: 74370

African (AFR) AF: 0.641 AC: 26556 AN: 41452

American (AMR) AF: 0.514 AC: 7862 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1425 AN: 3468

East Asian (EAS) AF: 0.679 AC: 3508 AN: 5170

South Asian (SAS) AF: 0.392 AC: 1890 AN: 4818

European-Finnish (FIN) AF: 0.191 AC: 2022 AN: 10608

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21839 AN: 67956

Other (OTH) AF: 0.425 AC: 897 AN: 2110

Alfa AF: 0.373 Hom.: 1501

Bravo AF: 0.470

Asia WGS AF: 0.506 AC: 1761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.15
DANN	Benign	0.13
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs7578618; hg19: chr2-191733357;