2-203889630-T-C

Variant names:

• chr2-203889630-T-C
• rs7600322
• ENST00000810800.1:n.64-7236T>C

Variant summary

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

The ENST00000810800.1(ENSG00000305408):​n.64-7236T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,988 control chromosomes in the GnomAD database, including 13,493 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 (13493 hom., cov: 31)
• Consequence: ENSG00000305408 ENST00000810800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 7 publications found

Genes affected

ENSG00000305408 (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 = 0.654 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
ENSG00000305408	ENST00000810800.1	n.64-7236T>C		intron_variant	Intron 1 of 2
ENSG00000305408	ENST00000810801.1	n.84-7236T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61623 AN: 151870 Hom.: 13500 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.405 AC: 61615 AN: 151988 Hom.: 13493 Cov.: 31 AF XY: 0.404 AC XY: 29989 AN XY: 74292

African (AFR) AF: 0.248 AC: 10268 AN: 41452

American (AMR) AF: 0.451 AC: 6885 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1840 AN: 3472

East Asian (EAS) AF: 0.297 AC: 1530 AN: 5158

South Asian (SAS) AF: 0.674 AC: 3243 AN: 4814

European-Finnish (FIN) AF: 0.343 AC: 3617 AN: 10560

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32692 AN: 67950

Other (OTH) AF: 0.467 AC: 987 AN: 2114

Alfa AF: 0.433 Hom.: 1837

Bravo AF: 0.400

Asia WGS AF: 0.507 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.85
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs7600322; hg19: chr2-204754353;