rs8038068

Variant names:

• chr15-43622175-T-C
• rs8038068
• ENST00000643290.1:n.86-3099A>G

Variant summary

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

The ENST00000643290.1(ENSG00000284772):​n.86-3099A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,548 control chromosomes in the GnomAD database, including 1,788 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 0.14 (1788 hom., cov: 31)
• Consequence: ENSG00000284772 ENST00000643290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434
• Publications: 7 publications found

Genes affected

ENSG00000284772 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643290.1. 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
	ENSG00000284772	ENST00000643290.1		n.86-3099A>G		intron	N/A	ENSP00000495476.1	A0A2R8Y6Q2
	ENSG00000309475	ENST00000841330.1		n.363+1572T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20595 AN: 151422 Hom.: 1787 Cov.: 31

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.136 AC: 20610 AN: 151548 Hom.: 1788 Cov.: 31 AF XY: 0.133 AC XY: 9838 AN XY: 73984

African (AFR) AF: 0.0872 AC: 3616 AN: 41480

American (AMR) AF: 0.133 AC: 2028 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3466

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5162

South Asian (SAS) AF: 0.170 AC: 751 AN: 4406

European-Finnish (FIN) AF: 0.104 AC: 1094 AN: 10564

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11952 AN: 67902

Other (OTH) AF: 0.152 AC: 320 AN: 2110

Alfa AF: 0.149 Hom.: 250

Bravo AF: 0.134

Asia WGS AF: 0.0740 AC: 261 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.5
DANN	Benign	0.86
PhyloP100		0.43
Mutation Taster		=100/0	polymorphism (auto)

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: rs8038068;

hg19: chr15-43914373;