8-72523859-A-G

Position:

• chr8-72523859-A-G

Variant summary

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

The XR_929042.3(LOC105375897):​n.798-6401T>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 0.43 in 152,140 control chromosomes in the GnomAD database, including 17,410 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 0.43 (17410 hom., cov: 32)
• Consequence: LOC105375897 XR_929042.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.797

Genes affected

LOC105375897 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375897	XR_929042.3	n.798-6401T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65436 AN: 152022 Hom.: 17398 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.430 AC: 65469 AN: 152140 Hom.: 17410 Cov.: 32 AF XY: 0.432 AC XY: 32126 AN XY: 74370

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.433

Alfa AF: 0.538 Hom.: 29154

Bravo AF: 0.419

Asia WGS AF: 0.321 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	10
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12550268; hg19: chr8-73436094;