chr8-2797033-C-T

Position:

• chr8-2797033-C-T

Variant summary

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

The NR_168443.1(LOC105377785):​n.539-7553C>T 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 0.363 in 151,970 control chromosomes in the GnomAD database, including 13,467 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 0.36 (13467 hom., cov: 31)
• Consequence: LOC105377785 NR_168443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377785	NR_168443.1	n.539-7553C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654515.1	n.532-7553C>T		intron_variant, non_coding_transcript_variant
	ENST00000520024.1	n.177-7553C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000662575.1	n.81+1658C>T		intron_variant, non_coding_transcript_variant
	ENST00000670600.1	n.539-7553C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55019 AN: 151856 Hom.: 13427 Cov.: 31

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.363 AC: 55120 AN: 151970 Hom.: 13467 Cov.: 31 AF XY: 0.365 AC XY: 27104 AN XY: 74290

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.332

Alfa AF: 0.249 Hom.: 2618

Bravo AF: 0.405

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1026374; hg19: chr8-2654569;