rs7010867

Positions:

• chr8-2813988-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.662+9279C>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 0.39 in 152,096 control chromosomes in the GnomAD database, including 14,392 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 0.39 (14392 hom., cov: 33)
• Consequence: LOC105377785 NR_168443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377785	NR_168443.1	n.662+9279C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654515.1	n.655+9279C>T		intron_variant, non_coding_transcript_variant
	ENST00000520024.1	n.369-5279C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000662575.1	n.206-5279C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59222 AN: 151978 Hom.: 14353 Cov.: 33

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.390 AC: 59319 AN: 152096 Hom.: 14392 Cov.: 33 AF XY: 0.391 AC XY: 29075 AN XY: 74322

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.367

Alfa AF: 0.271 Hom.: 12768

Bravo AF: 0.423

Asia WGS AF: 0.402 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7010867; hg19: chr8-2671510;