2-203898321-G-A

Variant names:

• chr2-203898321-G-A
• rs10197319
• ENST00000810800.1:n.203+1316G>A

Variant summary

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

The ENST00000810800.1(ENSG00000305408):​n.203+1316G>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 151,976 control chromosomes in the GnomAD database, including 14,790 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 (14790 hom., cov: 32)
• Consequence: ENSG00000305408 ENST00000810800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 13 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 = 0.501 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810800.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305408	ENST00000810800.1		n.203+1316G>A		intron	N/A
	ENSG00000305408	ENST00000810801.1		n.223+1316G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66325 AN: 151856 Hom.: 14784 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.437 AC: 66355 AN: 151976 Hom.: 14790 Cov.: 32 AF XY: 0.432 AC XY: 32123 AN XY: 74288

African (AFR) AF: 0.421 AC: 17453 AN: 41440

American (AMR) AF: 0.414 AC: 6311 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1802 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1224 AN: 5168

South Asian (SAS) AF: 0.517 AC: 2491 AN: 4814

European-Finnish (FIN) AF: 0.357 AC: 3763 AN: 10554

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31749 AN: 67964

Other (OTH) AF: 0.462 AC: 974 AN: 2106

Alfa AF: 0.461 Hom.: 51281

Bravo AF: 0.438

Asia WGS AF: 0.410 AC: 1426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.50
PhyloP100		-0.028

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10197319;

hg19: chr2-204763044;