8-2920519-T-C

Position:

• chr8-2920519-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+82755T>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 0.0795 in 152,270 control chromosomes in the GnomAD database, including 531 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 0.079 (531 hom., cov: 32)
• Consequence: LOC105377785 NR_168443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

LOC105377785 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377785	NR_168443.1	n.1171+82755T>C		intron_variant, non_coding_transcript_variant
LOC124901871	XR_007060785.1	n.75+3043A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 12094 AN: 152152 Hom.: 531 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0694

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0869

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.0795 AC: 12104 AN: 152270 Hom.: 531 Cov.: 32 AF XY: 0.0779 AC XY: 5802 AN XY: 74448

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0693

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.0872

Gnomad4 FIN AF: 0.0399

Gnomad4 NFE AF: 0.0686

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.0655 Hom.: 309

Bravo AF: 0.0834

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.77
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6989916; hg19: chr8-2778041;