ENST00000419462.1:n.285+961A>C

Variant names:

• chr8-101363039-A-C
• rs16867579
• ENST00000419462.2:n.285+961A>C

Variant summary

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

The ENST00000419462.2(ENSG00000293064):​n.285+961A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,156 control chromosomes in the GnomAD database, including 2,528 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 0.11 (2528 hom., cov: 32)
• Consequence: ENSG00000293064 ENST00000419462.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 3 publications found

Genes affected

ENSG00000293064 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419462.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293064	ENST00000419462.2	TSL:2	n.285+961A>C		intron	N/A
	ENSG00000293064	ENST00000737279.1		n.485-4584A>C		intron	N/A
	ENSG00000293064	ENST00000737284.1		n.162+961A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16192 AN: 152038 Hom.: 2504 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0537

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.00886

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.00594

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.00898

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.107 AC: 16270 AN: 152156 Hom.: 2528 Cov.: 32 AF XY: 0.105 AC XY: 7783 AN XY: 74394

African (AFR) AF: 0.344 AC: 14240 AN: 41428

American (AMR) AF: 0.0535 AC: 819 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3470

East Asian (EAS) AF: 0.00888 AC: 46 AN: 5178

South Asian (SAS) AF: 0.0188 AC: 91 AN: 4828

European-Finnish (FIN) AF: 0.00594 AC: 63 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.00898 AC: 611 AN: 68018

Other (OTH) AF: 0.0909 AC: 192 AN: 2112

Alfa AF: 0.0409 Hom.: 1989

Bravo AF: 0.122

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.70
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs16867579; hg19: chr8-102375267;