rs10877969

chr12-63153459-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000624438.1(ENSG00000279444):n.187-401T>C variant causes a intron, non coding transcript 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: ENST00000624438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.957

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000624438.1	n.187-401T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.217

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10877969; hg19: chr12-63547239;