rs1427547

Variant names:

• chr2-19540215-T-C
• rs1427547
• ENST00000822227.1:n.249-7135A>G

Variant summary

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

The ENST00000822227.1(ENSG00000306962):​n.249-7135A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,962 control chromosomes in the GnomAD database, including 28,376 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 0.61 (28376 hom., cov: 31)
• Consequence: ENSG00000306962 ENST00000822227.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 4 publications found

Genes affected

ENSG00000306962 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 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
ENSG00000306962	ENST00000822227.1	n.249-7135A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91934 AN: 151844 Hom.: 28333 Cov.: 31

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.606 AC: 92028 AN: 151962 Hom.: 28376 Cov.: 31 AF XY: 0.605 AC XY: 44933 AN XY: 74248

African (AFR) AF: 0.649 AC: 26903 AN: 41444

American (AMR) AF: 0.644 AC: 9839 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1660 AN: 3468

East Asian (EAS) AF: 0.806 AC: 4155 AN: 5152

South Asian (SAS) AF: 0.610 AC: 2935 AN: 4810

European-Finnish (FIN) AF: 0.542 AC: 5720 AN: 10552

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39034 AN: 67942

Other (OTH) AF: 0.581 AC: 1226 AN: 2110

Alfa AF: 0.582 Hom.: 13711

Bravo AF: 0.614

Asia WGS AF: 0.708 AC: 2460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.13
DANN	Benign	0.60
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1427547; hg19: chr2-19739976;