rs1786342

Variant names:

• chr8-100664135-T-C
• rs1786342
• XR_001746019.2:n.125+447T>C

Variant summary

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

The XR_001746019.2(LOC105375672):​n.125+447T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,004 control chromosomes in the GnomAD database, including 20,457 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 0.50 (20457 hom., cov: 31)
• Consequence: LOC105375672 XR_001746019.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 8 publications found

Genes affected

LOC105375672 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75719 AN: 151886 Hom.: 20413 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.499 AC: 75835 AN: 152004 Hom.: 20457 Cov.: 31 AF XY: 0.496 AC XY: 36823 AN XY: 74292

African (AFR) AF: 0.717 AC: 29722 AN: 41472

American (AMR) AF: 0.545 AC: 8321 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1417 AN: 3466

East Asian (EAS) AF: 0.415 AC: 2147 AN: 5172

South Asian (SAS) AF: 0.382 AC: 1836 AN: 4812

European-Finnish (FIN) AF: 0.361 AC: 3812 AN: 10552

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27064 AN: 67952

Other (OTH) AF: 0.486 AC: 1025 AN: 2108

Alfa AF: 0.432 Hom.: 62775

Bravo AF: 0.523

Asia WGS AF: 0.422 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.7
DANN	Benign	0.84
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1786342; hg19: chr8-101676363;