chr2-75313470-A-G

Variant names:

• chr2-75313470-A-G
• rs10515919
• ENST00000821156.1:n.249-34223T>C

Variant summary

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

The ENST00000821156.1(ENSG00000306791):​n.249-34223T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,086 control chromosomes in the GnomAD database, including 3,738 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 0.21 (3738 hom., cov: 32)
• Consequence: ENSG00000306791 ENST00000821156.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.864
• Publications: 4 publications found

Genes affected

ENSG00000306791 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 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
ENSG00000306791	ENST00000821156.1	n.249-34223T>C		intron_variant	Intron 1 of 2
ENSG00000306791	ENST00000821157.1	n.173-38333T>C		intron_variant	Intron 1 of 1
ENSG00000306811	ENST00000821263.1	n.146+21325A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32110 AN: 151968 Hom.: 3735 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.211 AC: 32141 AN: 152086 Hom.: 3738 Cov.: 32 AF XY: 0.216 AC XY: 16064 AN XY: 74336

African (AFR) AF: 0.188 AC: 7827 AN: 41526

American (AMR) AF: 0.307 AC: 4686 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 373 AN: 3462

East Asian (EAS) AF: 0.323 AC: 1664 AN: 5148

South Asian (SAS) AF: 0.167 AC: 801 AN: 4810

European-Finnish (FIN) AF: 0.332 AC: 3507 AN: 10574

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12622 AN: 67966

Other (OTH) AF: 0.187 AC: 395 AN: 2112

Alfa AF: 0.191 Hom.: 2240

Bravo AF: 0.213

Asia WGS AF: 0.249 AC: 867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.1
DANN	Benign	0.83
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs10515919; hg19: chr2-75540596;