chr8-16579752-T-C

Position:

• chr8-16579752-T-C

Variant summary

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

The XR_007061175.1(LOC101929028):​n.873-67842A>G 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 0.449 in 151,712 control chromosomes in the GnomAD database, including 15,706 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 0.45 (15706 hom., cov: 32)
• Consequence: LOC101929028 XR_007061175.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

Genes affected

LOC101929028 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929028	XR_007061175.1	n.873-67842A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68028 AN: 151594 Hom.: 15697 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.449 AC: 68071 AN: 151712 Hom.: 15706 Cov.: 32 AF XY: 0.448 AC XY: 33222 AN XY: 74158

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.490

Alfa AF: 0.484 Hom.: 23283

Bravo AF: 0.444

Asia WGS AF: 0.607 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.40
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs822318; hg19: chr8-16437261;