chr2-62289409-C-A

Variant names:

• chr2-62289409-C-A
• rs6713082
• ENST00000807679.1:n.302+13822C>A

Variant summary

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

The ENST00000807679.1(ENSG00000228541):​n.302+13822C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,296 control chromosomes in the GnomAD database, including 2,790 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 0.17 (2790 hom., cov: 32)
• Consequence: ENSG00000228541 ENST00000807679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 9 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.238 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
ENSG00000228541	ENST00000807679.1	n.302+13822C>A		intron_variant	Intron 3 of 5
ENSG00000228541	ENST00000807680.1	n.298+13822C>A		intron_variant	Intron 3 of 6
ENSG00000228541	ENST00000807681.1	n.282+13822C>A		intron_variant	Intron 3 of 5
ENSG00000305072	ENST00000808384.1	n.110+4011G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25739 AN: 152178 Hom.: 2798 Cov.: 32

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.169 AC: 25715 AN: 152296 Hom.: 2790 Cov.: 32 AF XY: 0.166 AC XY: 12362 AN XY: 74456

African (AFR) AF: 0.0444 AC: 1846 AN: 41578

American (AMR) AF: 0.199 AC: 3039 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 969 AN: 3472

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5184

South Asian (SAS) AF: 0.138 AC: 667 AN: 4820

European-Finnish (FIN) AF: 0.204 AC: 2167 AN: 10608

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16398 AN: 68014

Other (OTH) AF: 0.180 AC: 381 AN: 2114

Alfa AF: 0.222 Hom.: 11164

Bravo AF: 0.164

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.44
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs6713082; hg19: chr2-62516544;