chr8-25709572-G-A

Variant names:

• chr8-25709572-G-A
• rs6986695
• XR_001745849.2:n.238+79203G>A

Variant summary

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

The XR_001745849.2(LOC107986933):​n.238+79203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,928 control chromosomes in the GnomAD database, including 5,695 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 0.27 (5695 hom., cov: 32)
• Consequence: LOC107986933 XR_001745849.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 2 publications found

Genes affected

LOC107986933 (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 (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986933	XR_001745849.2	n.238+79203G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40642 AN: 151808 Hom.: 5685 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.268 AC: 40697 AN: 151928 Hom.: 5695 Cov.: 32 AF XY: 0.265 AC XY: 19700 AN XY: 74254

African (AFR) AF: 0.342 AC: 14172 AN: 41430

American (AMR) AF: 0.240 AC: 3665 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1237 AN: 5162

South Asian (SAS) AF: 0.159 AC: 763 AN: 4810

European-Finnish (FIN) AF: 0.247 AC: 2601 AN: 10548

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16877 AN: 67924

Other (OTH) AF: 0.233 AC: 491 AN: 2108

Alfa AF: 0.249 Hom.: 3740

Bravo AF: 0.272

Asia WGS AF: 0.228 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.51
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs6986695; hg19: chr8-25567088;