ENST00000650061.1:n.326+314C>T

Variant names:

• chr8-1962492-G-A
• rs12547074
• ENST00000650061.1:n.326+314C>T

Variant summary

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

The ENST00000650061.1(ENSG00000285957):​n.326+314C>T variant causes a intron 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: ENSG00000285957 ENST00000650061.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 4 publications found

Genes affected

ENSG00000285957 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285957	ENST00000650061.1	n.326+314C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.913 AC: 37936 AN: 41554

American (AMR) AF: 0.933 AC: 14278 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3298 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5138 AN: 5148

South Asian (SAS) AF: 0.985 AC: 4755 AN: 4828

European-Finnish (FIN) AF: 0.968 AC: 10284 AN: 10622

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.935 AC: 63619 AN: 68026

Other (OTH) AF: 0.928 AC: 1959 AN: 2112

Alfa AF: 0.936 Hom.: 17114

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12547074; hg19: chr8-1910658;