chr8-83683361-G-T

Position:

• chr8-83683361-G-T

Variant summary

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

The XR_001745724.1(LOC105375932):​n.200+3089C>A 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 0.638 in 151,774 control chromosomes in the GnomAD database, including 32,618 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 0.64 (32618 hom., cov: 31)
• Consequence: LOC105375932 XR_001745724.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

Genes affected

LOC105375932 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375932	XR_001745724.1	n.200+3089C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96784 AN: 151656 Hom.: 32562 Cov.: 31

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.638 AC: 96897 AN: 151774 Hom.: 32618 Cov.: 31 AF XY: 0.634 AC XY: 47015 AN XY: 74204

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.605

Alfa AF: 0.597 Hom.: 9815

Bravo AF: 0.662

Asia WGS AF: 0.667 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6473464; hg19: chr8-84595596;