rs6984609

Positions:

• chr8-48677025-A-G

Variant summary

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

The NR_105002.1(LOC101929268):​n.357-18399A>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 0.179 in 152,088 control chromosomes in the GnomAD database, including 5,329 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 0.18 (5329 hom., cov: 32)
• Consequence: LOC101929268 NR_105002.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

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 = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929268	NR_105002.1	n.357-18399A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522575.1	n.357-18399A>G		intron_variant, non_coding_transcript_variant		2
	ENST00000654201.1	n.58-17726A>G		intron_variant, non_coding_transcript_variant
	ENST00000657307.1	n.24+17842A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27254 AN: 151970 Hom.: 5321 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.0350

Gnomad FIN AF: 0.00952

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0506

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.179 AC: 27292 AN: 152088 Hom.: 5329 Cov.: 32 AF XY: 0.172 AC XY: 12806 AN XY: 74382

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.0828

Gnomad4 EAS AF: 0.0650

Gnomad4 SAS AF: 0.0336

Gnomad4 FIN AF: 0.00952

Gnomad4 NFE AF: 0.0506

Gnomad4 OTH AF: 0.176

Alfa AF: 0.0757 Hom.: 1544

Bravo AF: 0.206

Asia WGS AF: 0.0750 AC: 263 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	0.97
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6984609; hg19: chr8-49589585;