rs1472962

Variant names:

• chr4-94671226-G-A
• rs1472962
• ENST00000719651.1:n.105G>A

Variant summary

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

The ENST00000719651.1(ENSG00000293888):​n.105G>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 0.612 in 152,064 control chromosomes in the GnomAD database, including 29,127 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 (29127 hom., cov: 32)
• Consequence: ENSG00000293888 ENST00000719651.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 11 publications found

Genes affected

ENSG00000293888 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 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
ENSG00000293888	ENST00000719651.1	n.105G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92987 AN: 151946 Hom.: 29094 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.612 AC: 93071 AN: 152064 Hom.: 29127 Cov.: 32 AF XY: 0.604 AC XY: 44924 AN XY: 74320

African (AFR) AF: 0.733 AC: 30419 AN: 41476

American (AMR) AF: 0.610 AC: 9326 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3470

East Asian (EAS) AF: 0.586 AC: 3026 AN: 5162

South Asian (SAS) AF: 0.374 AC: 1803 AN: 4816

European-Finnish (FIN) AF: 0.510 AC: 5382 AN: 10552

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39592 AN: 67980

Other (OTH) AF: 0.608 AC: 1284 AN: 2112

Alfa AF: 0.590 Hom.: 15196

Bravo AF: 0.627

Asia WGS AF: 0.482 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.51
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1472962; hg19: chr4-95592377;