2-190820277-T-C

Variant names:

• chr2-190820277-T-C
• rs1882395
• ENST00000675274.1:n.45-4438A>G

Variant summary

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

The ENST00000675274.1(ENSG00000228509):​n.45-4438A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,010 control chromosomes in the GnomAD database, including 11,159 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 0.37 (11159 hom., cov: 31)
• Consequence: ENSG00000228509 ENST00000675274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 5 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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 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	ENST00000675274.1	n.45-4438A>G		intron_variant	Intron 1 of 2
ENSG00000228509	ENST00000676095.2	n.83-4438A>G		intron_variant	Intron 1 of 8
ENSG00000228509	ENST00000676152.1	n.144-4438A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55575 AN: 151892 Hom.: 11162 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.366 AC: 55579 AN: 152010 Hom.: 11159 Cov.: 31 AF XY: 0.356 AC XY: 26416 AN XY: 74274

African (AFR) AF: 0.224 AC: 9281 AN: 41488

American (AMR) AF: 0.318 AC: 4856 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1615 AN: 3468

East Asian (EAS) AF: 0.302 AC: 1560 AN: 5168

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4822

European-Finnish (FIN) AF: 0.350 AC: 3686 AN: 10534

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32061 AN: 67948

Other (OTH) AF: 0.373 AC: 787 AN: 2112

Alfa AF: 0.402 Hom.: 1599

Bravo AF: 0.361

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.6
DANN	Benign	0.68
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1882395; hg19: chr2-191685003;