8-97156475-C-T

Position:

• chr8-97156475-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.472-202865G>A 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 0.236 in 151,974 control chromosomes in the GnomAD database, including 4,649 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 0.24 (4649 hom., cov: 32)
• Consequence: LOC101927066 NR_125390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

Genes affected

LOC101927066 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927066	NR_125390.1	n.472-202865G>A		intron_variant, non_coding_transcript_variant
LOC105375655	XR_928434.3	n.174+5803C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35917 AN: 151858 Hom.: 4652 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.236 AC: 35923 AN: 151974 Hom.: 4649 Cov.: 32 AF XY: 0.240 AC XY: 17830 AN XY: 74264

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.240

Alfa AF: 0.201 Hom.: 4341

Bravo AF: 0.235

Asia WGS AF: 0.422 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs982502; hg19: chr8-98168703;