rs11174815

chr12-63153316-G-Achr12-63153316-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000624438.1(ENSG00000279444):n.187-544G>A 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 0.0119 in 137,708 control chromosomes in the GnomAD database, including 12 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 0.012 (12 hom., cov: 20)
• Consequence: ENST00000624438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 13 gene

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.187-544G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0161

Gnomad4 AMR AF: 0.00874

Gnomad4 ASJ AF: 0.0175

Gnomad4 EAS AF: 0.00187

Gnomad4 SAS AF: 0.0202

Gnomad4 FIN AF: 0.00283

Gnomad4 NFE AF: 0.0119

Gnomad4 OTH AF: 0.0123

Alfa AF: 0.00481 Hom.: 0

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

Splicing

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

Publications

LitVar

Other links and lift over

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