8-97157837-C-T

Variant names:

• chr8-97157837-C-T
• rs987036
• NR_125390.1:n.472-204227G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125390.1(LOC101927066):​n.472-204227G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 151,876 control chromosomes in the GnomAD database, including 42,505 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 0.74 (42505 hom., cov: 30)
• Consequence: LOC101927066 NR_125390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 1 publications found

Genes affected

LOC101927066 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927066	NR_125390.1	n.472-204227G>A		intron_variant	Intron 2 of 2
LOC105375655	XR_928434.3	n.174+7165C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112767 AN: 151758 Hom.: 42451 Cov.: 30

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.743 AC: 112886 AN: 151876 Hom.: 42505 Cov.: 30 AF XY: 0.739 AC XY: 54881 AN XY: 74230

African (AFR) AF: 0.732 AC: 30286 AN: 41356

American (AMR) AF: 0.756 AC: 11539 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2581 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1861 AN: 5152

South Asian (SAS) AF: 0.549 AC: 2631 AN: 4794

European-Finnish (FIN) AF: 0.789 AC: 8344 AN: 10570

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53113 AN: 67966

Other (OTH) AF: 0.723 AC: 1522 AN: 2106

Alfa AF: 0.755 Hom.: 19425

Bravo AF: 0.743

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.80
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs987036; hg19: chr8-98170065;