chr8-2876680-T-C

Position:

• chr8-2876680-T-C

Variant summary

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

The NR_168443.1(LOC105377785):​n.1171+38916T>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 0.196 in 152,198 control chromosomes in the GnomAD database, including 4,550 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 0.20 (4550 hom., cov: 33)
• Consequence: LOC105377785 NR_168443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377785	NR_168443.1	n.1171+38916T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656456.1	n.45+1192A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29833 AN: 152080 Hom.: 4540 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.0349

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.196 AC: 29890 AN: 152198 Hom.: 4550 Cov.: 33 AF XY: 0.195 AC XY: 14489 AN XY: 74432

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.0349

Gnomad4 NFE AF: 0.0881

Gnomad4 OTH AF: 0.214

Alfa AF: 0.113 Hom.: 2191

Bravo AF: 0.215

Asia WGS AF: 0.305 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs341672; hg19: chr8-2734202;