8-82161594-C-T

Variant names:

• chr8-82161594-C-T
• rs13264970
• ENST00000659043.1:n.145+87870C>T

Variant summary

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

The ENST00000659043.1(ENSG00000254394):​n.145+87870C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,028 control chromosomes in the GnomAD database, including 31,115 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 0.62 (31115 hom., cov: 32)
• Consequence: ENSG00000254394 ENST00000659043.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 8 publications found

Genes affected

ENSG00000254394 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659043.1. 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
	ENSG00000254394	ENST00000659043.1		n.145+87870C>T		intron	N/A
	ENSG00000254394	ENST00000663058.1		n.392+87870C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94213 AN: 151912 Hom.: 31113 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.620 AC: 94223 AN: 152028 Hom.: 31115 Cov.: 32 AF XY: 0.623 AC XY: 46264 AN XY: 74296

African (AFR) AF: 0.374 AC: 15519 AN: 41446

American (AMR) AF: 0.708 AC: 10807 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2332 AN: 3472

East Asian (EAS) AF: 0.600 AC: 3095 AN: 5162

South Asian (SAS) AF: 0.686 AC: 3301 AN: 4814

European-Finnish (FIN) AF: 0.686 AC: 7243 AN: 10566

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49689 AN: 67990

Other (OTH) AF: 0.651 AC: 1373 AN: 2110

Alfa AF: 0.700 Hom.: 65974

Bravo AF: 0.613

Asia WGS AF: 0.568 AC: 1978 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.75
PhyloP100		-0.17

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13264970;

hg19: chr8-83073829;