2-104366809-G-A

Variant names:

• chr2-104366809-G-A
• rs7570682
• ENST00000758996.1:n.238+27016C>T

Variant summary

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

The ENST00000758996.1(ENSG00000298919):​n.238+27016C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,938 control chromosomes in the GnomAD database, including 8,278 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 0.31 (8278 hom., cov: 32)
• Consequence: ENSG00000298919 ENST00000758996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 14 publications found

Genes affected

ENSG00000298919 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758996.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298919	ENST00000758996.1		n.238+27016C>T		intron	N/A
	ENSG00000298919	ENST00000758997.1		n.266+27016C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46647 AN: 151820 Hom.: 8252 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.308 AC: 46729 AN: 151938 Hom.: 8278 Cov.: 32 AF XY: 0.305 AC XY: 22643 AN XY: 74288

African (AFR) AF: 0.491 AC: 20327 AN: 41418

American (AMR) AF: 0.296 AC: 4516 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3466

East Asian (EAS) AF: 0.381 AC: 1963 AN: 5156

South Asian (SAS) AF: 0.128 AC: 618 AN: 4814

European-Finnish (FIN) AF: 0.244 AC: 2576 AN: 10536

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15254 AN: 67952

Other (OTH) AF: 0.290 AC: 611 AN: 2110

Alfa AF: 0.243 Hom.: 21501

Bravo AF: 0.322

Asia WGS AF: 0.317 AC: 1102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.19
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs7570682; hg19: chr2-104983267;