rs1786342

Positions:

• chr8-100664135-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746019.2(LOC105375672):​n.125+447T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

Genes affected

LOC105375672 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375672	XR_001746019.2	n.125+447T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.486

Alfa AF: 0.418 Hom.: 28165

Bravo AF: 0.523

Asia WGS AF: 0.422 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1786342; hg19: chr8-101676363;