rs12547074

Positions:

• chr8-1962492-G-A
• chr8-1962492-G-C
• chr8-1962492-G-T

Variant summary

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

The ENST00000650061.1(ENSG00000285957):​n.326+314C>T 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 0.935 in 152,276 control chromosomes in the GnomAD database, including 66,669 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 0.94 (66669 hom., cov: 33)
• Consequence: ENST00000650061.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650061.1	n.326+314C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.935 AC: 142324 AN: 152158 Hom.: 66609 Cov.: 33

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.991

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.985

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.935 AC: 142443 AN: 152276 Hom.: 66669 Cov.: 33 AF XY: 0.939 AC XY: 69889 AN XY: 74446

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.933

Gnomad4 ASJ AF: 0.950

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.985

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.935

Gnomad4 OTH AF: 0.928

Alfa AF: 0.937 Hom.: 13417

Bravo AF: 0.931

Asia WGS AF: 0.986 AC: 3430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.25
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12547074; hg19: chr8-1910658;