chr8-138041126-C-T

Variant names:

• chr8-138041126-C-T
• rs6986279
• ENST00000518973.1:n.514+41931G>A

Variant summary

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

The ENST00000518973.1(ENSG00000253288):​n.514+41931G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,180 control chromosomes in the GnomAD database, including 35,618 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 0.67 (35618 hom., cov: 33)
• Consequence: ENSG00000253288 ENST00000518973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 publications found

Genes affected

ENSG00000253288 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518973.1. 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
	LOC401478	NR_161374.1		n.490-704G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253288	ENST00000518973.1	TSL:2	n.514+41931G>A		intron	N/A
	ENSG00000253288	ENST00000657186.1		n.601+41931G>A		intron	N/A
	ENSG00000254361	ENST00000716518.1		n.621+21445C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101555 AN: 152062 Hom.: 35555 Cov.: 33

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.668 AC: 101678 AN: 152180 Hom.: 35618 Cov.: 33 AF XY: 0.676 AC XY: 50310 AN XY: 74392

African (AFR) AF: 0.842 AC: 34980 AN: 41542

American (AMR) AF: 0.717 AC: 10956 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1894 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5152 AN: 5174

South Asian (SAS) AF: 0.773 AC: 3734 AN: 4832

European-Finnish (FIN) AF: 0.585 AC: 6184 AN: 10568

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36612 AN: 67992

Other (OTH) AF: 0.654 AC: 1382 AN: 2112

Alfa AF: 0.598 Hom.: 15712

Bravo AF: 0.687

Asia WGS AF: 0.876 AC: 3044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.019
DANN	Benign	0.17
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6986279; hg19: chr8-139053369;