ENST00000447571.5:n.1261G>A

Variant names:

• chr2-47942243-C-T
• rs34198350
• ENST00000447571.5:n.1261G>A

Variant summary

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

The ENST00000447571.5(ENSG00000230773):​n.1261G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0945 in 152,320 control chromosomes in the GnomAD database, including 772 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 0.094 (771 hom., cov: 32)
  • Exomes 𝑓: 0.14 (1 hom.)
• Consequence: ENSG00000230773 ENST00000447571.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 5 publications found

Genes affected

ENSG00000230773 (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 (NFE) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447571.5. 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
	ENSG00000230773	ENST00000447571.5	TSL:1	n.1261G>A		non_coding_transcript_exon	Exon 9 of 9
	ENSG00000230773	ENST00000651429.1		n.807+6724G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0944 AC: 14362 AN: 152084 Hom.: 766 Cov.: 32

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0377

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0195

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0936

GnomAD4 exome AF: 0.136 AC: 16 AN: 118 Hom.: 1 Cov.: 0 AF XY: 0.146 AC XY: 14 AN XY: 96

African (AFR) AF: 0.100 AC: 1 AN: 10

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.143 AC: 14 AN: 98

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.0945 AC: 14383 AN: 152202 Hom.: 771 Cov.: 32 AF XY: 0.0933 AC XY: 6943 AN XY: 74410

African (AFR) AF: 0.0833 AC: 3458 AN: 41520

American (AMR) AF: 0.0630 AC: 964 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0377 AC: 131 AN: 3472

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5174

South Asian (SAS) AF: 0.0199 AC: 96 AN: 4822

European-Finnish (FIN) AF: 0.154 AC: 1632 AN: 10588

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7855 AN: 68014

Other (OTH) AF: 0.0922 AC: 195 AN: 2116

Alfa AF: 0.0997 Hom.: 296

Bravo AF: 0.0868

Asia WGS AF: 0.0180 AC: 64 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	3.9
DANN	Benign	0.74
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs34198350; hg19: chr2-48169382;