2-127127018-C-A

Variant names:

• chr2-127127018-C-A
• rs6431221
• ENST00000726607.1:n.342-8242C>A

Variant summary

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

The ENST00000726607.1(ENSG00000294899):​n.342-8242C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,888 control chromosomes in the GnomAD database, including 20,295 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 0.52 (20295 hom., cov: 31)
• Consequence: ENSG00000294899 ENST00000726607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 4 publications found

Genes affected

ENSG00000294899 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726607.1. 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
	ENSG00000294899	ENST00000726607.1		n.342-8242C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78235 AN: 151770 Hom.: 20287 Cov.: 31

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.515 AC: 78274 AN: 151888 Hom.: 20295 Cov.: 31 AF XY: 0.516 AC XY: 38282 AN XY: 74234

African (AFR) AF: 0.547 AC: 22629 AN: 41396

American (AMR) AF: 0.490 AC: 7489 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2453 AN: 5166

South Asian (SAS) AF: 0.637 AC: 3069 AN: 4816

European-Finnish (FIN) AF: 0.493 AC: 5199 AN: 10536

Middle Eastern (MID) AF: 0.490 AC: 142 AN: 290

European-Non Finnish (NFE) AF: 0.508 AC: 34516 AN: 67924

Other (OTH) AF: 0.493 AC: 1039 AN: 2106

Alfa AF: 0.506 Hom.: 7192

Bravo AF: 0.508

Asia WGS AF: 0.551 AC: 1916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.27
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs6431221; hg19: chr2-127884594;