chr2-62530420-G-A

Variant names:

• chr2-62530420-G-A
• rs1997247
• ENST00000807713.1:n.332+29097G>A

Variant summary

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

The ENST00000807713.1(ENSG00000228541):​n.332+29097G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0994 in 152,238 control chromosomes in the GnomAD database, including 851 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 0.099 (851 hom., cov: 33)
• Consequence: ENSG00000228541 ENST00000807713.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 3 publications found

Genes affected

ENSG00000228541 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807713.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228541	ENST00000807713.1		n.332+29097G>A		intron	N/A
	ENSG00000228541	ENST00000807714.1		n.229-24702G>A		intron	N/A
	ENSG00000228541	ENST00000807715.1		n.242+29097G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0995 AC: 15132 AN: 152120 Hom.: 852 Cov.: 33

Gnomad AFR AF: 0.0389

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0994 AC: 15131 AN: 152238 Hom.: 851 Cov.: 33 AF XY: 0.100 AC XY: 7462 AN XY: 74470

African (AFR) AF: 0.0388 AC: 1610 AN: 41546

American (AMR) AF: 0.101 AC: 1538 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1127 AN: 5176

South Asian (SAS) AF: 0.126 AC: 608 AN: 4826

European-Finnish (FIN) AF: 0.118 AC: 1251 AN: 10606

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8519 AN: 68014

Other (OTH) AF: 0.101 AC: 214 AN: 2112

Alfa AF: 0.121 Hom.: 1276

Bravo AF: 0.0936

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.20
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs1997247; hg19: chr2-62757555;