rs6468544

Positions:

• chr8-97317537-C-G
• chr8-97317537-C-T

Variant summary

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

The NR_125390.1(LOC101927066):​n.471+101533G>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 0.305 in 152,016 control chromosomes in the GnomAD database, including 7,577 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 0.31 (7577 hom., cov: 32)
• Consequence: LOC101927066 NR_125390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781

Genes affected

LOC101927066 (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 = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927066	NR_125390.1	n.471+101533G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46358 AN: 151898 Hom.: 7568 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.305 AC: 46406 AN: 152016 Hom.: 7577 Cov.: 32 AF XY: 0.300 AC XY: 22290 AN XY: 74312

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.0200

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.283

Alfa AF: 0.167 Hom.: 335

Bravo AF: 0.300

Asia WGS AF: 0.107 AC: 374 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	7.9
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6468544; hg19: chr8-98329765;