rs1866347

Variant names:

• chr8-23689997-G-A
• rs1866347
• XR_001745842.2:n.1312+21247G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-23689997-G-A
• chr8-23689997-G-C

Variant summary

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

The XR_001745842.2(LOC107986930):​n.1312+21247G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,060 control chromosomes in the GnomAD database, including 6,978 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 0.28 (6978 hom., cov: 31)
• Consequence: LOC107986930 XR_001745842.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 3 publications found

Genes affected

LOC107986930 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986930	XR_001745842.2	n.1312+21247G>A		intron_variant	Intron 3 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42300 AN: 151942 Hom.: 6963 Cov.: 31

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.279 AC: 42368 AN: 152060 Hom.: 6978 Cov.: 31 AF XY: 0.277 AC XY: 20589 AN XY: 74324

African (AFR) AF: 0.451 AC: 18703 AN: 41448

American (AMR) AF: 0.263 AC: 4024 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3468

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5180

South Asian (SAS) AF: 0.240 AC: 1160 AN: 4826

European-Finnish (FIN) AF: 0.243 AC: 2568 AN: 10554

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.213 AC: 14465 AN: 67978

Other (OTH) AF: 0.247 AC: 522 AN: 2110

Alfa AF: 0.220 Hom.: 12600

Bravo AF: 0.285

Asia WGS AF: 0.200 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.35
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1866347; hg19: chr8-23547510;