rs10877969

Variant names:

• chr12-63153459-T-C
• rs10877969
• ENST00000624438.1:n.187-401T>C

Variant summary

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

The ENST00000624438.1(ENSG00000279444):​n.187-401T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,072 control chromosomes in the GnomAD database, including 7,709 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 0.26 (7709 hom., cov: 32)
• Consequence: ENSG00000279444 ENST00000624438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.957
• Publications: 27 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 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
ENSG00000279444	ENST00000624438.1	n.187-401T>C		intron_variant	Intron 2 of 2	5
ENSG00000302777	ENST00000789492.1	n.498-401T>C		intron_variant	Intron 2 of 2
ENSG00000302777	ENST00000789493.1	n.409-401T>C		intron_variant	Intron 2 of 2
ENSG00000302754	ENST00000789342.1	n.*180A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39076 AN: 151956 Hom.: 7686 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.257 AC: 39139 AN: 152072 Hom.: 7709 Cov.: 32 AF XY: 0.254 AC XY: 18885 AN XY: 74366

African (AFR) AF: 0.550 AC: 22789 AN: 41420

American (AMR) AF: 0.152 AC: 2331 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3470

East Asian (EAS) AF: 0.149 AC: 769 AN: 5178

South Asian (SAS) AF: 0.277 AC: 1337 AN: 4824

European-Finnish (FIN) AF: 0.141 AC: 1493 AN: 10588

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9372 AN: 67990

Other (OTH) AF: 0.217 AC: 457 AN: 2110

Alfa AF: 0.205 Hom.: 837

Bravo AF: 0.265

Asia WGS AF: 0.256 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.46
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs10877969; hg19: chr12-63547239;