ENST00000624438.1:n.187-544G>A

Variant names:

• chr12-63153316-G-A
• rs11174815
• ENST00000624438.1:n.187-544G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000624438.1(ENSG00000279444):​n.187-544G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.012 (12 hom., cov: 20)
• Consequence: ENSG00000279444 ENST00000624438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 7 publications found

Genes affected

ENSG00000279444 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0119 (1645/137708) while in subpopulation SAS AF = 0.0202 (80/3970). AF 95% confidence interval is 0.0166. There are 12 homozygotes in GnomAd4. There are 761 alleles in the male GnomAd4 subpopulation. Median coverage is 20. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 12 gene

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
ENSG00000279444	ENST00000624438.1	n.187-544G>A		intron_variant	Intron 2 of 2	5
ENSG00000302777	ENST00000789492.1	n.498-544G>A		intron_variant	Intron 2 of 2
ENSG00000302777	ENST00000789493.1	n.409-544G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0120 AC: 1647 AN: 137620 Hom.: 13 Cov.: 20

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00875

Gnomad ASJ AF: 0.0175

Gnomad EAS AF: 0.00186

Gnomad SAS AF: 0.0196

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0134

Gnomad NFE AF: 0.0119

Gnomad OTH AF: 0.0130

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

GnomAD4 genome AF: 0.0119 AC: 1645 AN: 137708 Hom.: 12 Cov.: 20 AF XY: 0.0114 AC XY: 761 AN XY: 67038

African (AFR) AF: 0.0161 AC: 556 AN: 34478

American (AMR) AF: 0.00874 AC: 124 AN: 14188

Ashkenazi Jewish (ASJ) AF: 0.0175 AC: 59 AN: 3370

East Asian (EAS) AF: 0.00187 AC: 9 AN: 4816

South Asian (SAS) AF: 0.0202 AC: 80 AN: 3970

European-Finnish (FIN) AF: 0.00283 AC: 27 AN: 9530

Middle Eastern (MID) AF: 0.00719 AC: 2 AN: 278

European-Non Finnish (NFE) AF: 0.0119 AC: 764 AN: 64298

Other (OTH) AF: 0.0123 AC: 24 AN: 1948

Alfa AF: 0.00962 Hom.: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.16
DANN	Benign	0.33
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs11174815; hg19: chr12-63547096; COSMIC: COSV54546800;