8-59691634-T-C

Variant names:

• chr8-59691634-T-C
• rs16925150
• ENST00000796877.1:n.163-23244T>C

Variant summary

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

The ENST00000796877.1(ENSG00000303742):​n.163-23244T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0867 in 152,234 control chromosomes in the GnomAD database, including 1,402 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 0.087 (1402 hom., cov: 32)
• Consequence: ENSG00000303742 ENST00000796877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279
• Publications: 2 publications found

Genes affected

ENSG00000303742 (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 (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796877.1. 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
	ENSG00000303742	ENST00000796877.1		n.163-23244T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0865 AC: 13164 AN: 152116 Hom.: 1397 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0786

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.00623

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0867 AC: 13196 AN: 152234 Hom.: 1402 Cov.: 32 AF XY: 0.0887 AC XY: 6603 AN XY: 74460

African (AFR) AF: 0.231 AC: 9594 AN: 41504

American (AMR) AF: 0.0789 AC: 1207 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3470

East Asian (EAS) AF: 0.251 AC: 1301 AN: 5180

South Asian (SAS) AF: 0.0847 AC: 409 AN: 4828

European-Finnish (FIN) AF: 0.00226 AC: 24 AN: 10614

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.00623 AC: 424 AN: 68020

Other (OTH) AF: 0.0681 AC: 144 AN: 2116

Alfa AF: 0.0387 Hom.: 881

Bravo AF: 0.0974

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.62
PhyloP100		0.28

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: rs16925150;

hg19: chr8-60604193;