22-37203025-G-T

Variant names:

• chr22-37203025-G-T
• rs229562
• ENST00000723808.1:n.77C>A

Variant summary

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

The ENST00000723808.1(ENSG00000294472):​n.77C>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 0.652 in 152,080 control chromosomes in the GnomAD database, including 33,889 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 0.65 (33889 hom., cov: 32)
• Consequence: ENSG00000294472 ENST00000723808.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 10 publications found

Genes affected

ENSG00000294472 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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
ENSG00000294472	ENST00000723808.1	n.77C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99092 AN: 151962 Hom.: 33829 Cov.: 32

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.652 AC: 99213 AN: 152080 Hom.: 33889 Cov.: 32 AF XY: 0.651 AC XY: 48379 AN XY: 74338

African (AFR) AF: 0.851 AC: 35331 AN: 41504

American (AMR) AF: 0.667 AC: 10189 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2020 AN: 3468

East Asian (EAS) AF: 0.824 AC: 4248 AN: 5158

South Asian (SAS) AF: 0.660 AC: 3183 AN: 4822

European-Finnish (FIN) AF: 0.494 AC: 5228 AN: 10578

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36938 AN: 67952

Other (OTH) AF: 0.649 AC: 1373 AN: 2114

Alfa AF: 0.592 Hom.: 19612

Bravo AF: 0.676

Asia WGS AF: 0.775 AC: 2691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.52
DANN	Benign	0.62
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs229562; hg19: chr22-37599065; COSMIC: COSV60730453;