2-67681714-T-C

Variant names:

• chr2-67681714-T-C
• rs4671825
• ENST00000419809.1:n.126+2238A>G

Variant summary

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

The ENST00000419809.1(ENSG00000235495):​n.126+2238A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,932 control chromosomes in the GnomAD database, including 15,970 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 0.45 (15970 hom., cov: 31)
• Consequence: ENSG00000235495 ENST00000419809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 2 publications found

Genes affected

ENSG00000235495 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.531 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
ENSG00000235495	ENST00000419809.1	n.126+2238A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67755 AN: 151816 Hom.: 15957 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.446 AC: 67799 AN: 151932 Hom.: 15970 Cov.: 31 AF XY: 0.445 AC XY: 33087 AN XY: 74282

African (AFR) AF: 0.314 AC: 12997 AN: 41438

American (AMR) AF: 0.541 AC: 8250 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1628 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1311 AN: 5158

South Asian (SAS) AF: 0.487 AC: 2346 AN: 4818

European-Finnish (FIN) AF: 0.480 AC: 5068 AN: 10552

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34509 AN: 67920

Other (OTH) AF: 0.457 AC: 963 AN: 2108

Alfa AF: 0.476 Hom.: 3015

Bravo AF: 0.445

Asia WGS AF: 0.416 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.31
DANN	Benign	0.80
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4671825; hg19: chr2-67908846;