8-2879984-G-T

Variant names:

• chr8-2879984-G-T
• rs341676
• ENST00000725259.1:n.1166+42220G>T

Variant summary

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

The NR_168441.1(LOC105377785):​n.1166+42220G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.942 in 152,324 control chromosomes in the GnomAD database, including 67,692 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 0.94 (67692 hom., cov: 33)
• Consequence: LOC105377785 NR_168441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 2 publications found

Genes affected

ENSG00000253853 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377785	NR_168441.1	n.1166+42220G>T		intron_variant	Intron 6 of 11
LOC105377785	NR_168442.1	n.1330+32314G>T		intron_variant	Intron 7 of 14
LOC105377785	NR_168443.1	n.1171+42220G>T		intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253853	ENST00000725259.1	n.1166+42220G>T		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.942 AC: 143396 AN: 152206 Hom.: 67629 Cov.: 33

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.942 AC: 143518 AN: 152324 Hom.: 67692 Cov.: 33 AF XY: 0.942 AC XY: 70128 AN XY: 74484

African (AFR) AF: 0.975 AC: 40544 AN: 41576

American (AMR) AF: 0.946 AC: 14464 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3145 AN: 3472

East Asian (EAS) AF: 0.974 AC: 5055 AN: 5188

South Asian (SAS) AF: 0.922 AC: 4452 AN: 4830

European-Finnish (FIN) AF: 0.945 AC: 10031 AN: 10612

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62751 AN: 68028

Other (OTH) AF: 0.927 AC: 1961 AN: 2116

Alfa AF: 0.941 Hom.: 4784

Bravo AF: 0.944

Asia WGS AF: 0.940 AC: 3269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.27
DANN	Benign	0.49
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs341676; hg19: chr8-2737506;