8-97269961-G-A

Variant names:

• chr8-97269961-G-A
• rs1864729
• NR_125390.1:n.471+149109C>T

Variant summary

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

The NR_125390.1(LOC101927066):​n.471+149109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 151,990 control chromosomes in the GnomAD database, including 4,378 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 (4378 hom., cov: 32)
• Consequence: LOC101927066 NR_125390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 12 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_125390.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101927066	NR_125390.1		n.471+149109C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26736 AN: 151872 Hom.: 4376 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.176 AC: 26765 AN: 151990 Hom.: 4378 Cov.: 32 AF XY: 0.172 AC XY: 12801 AN XY: 74268

African (AFR) AF: 0.436 AC: 18063 AN: 41408

American (AMR) AF: 0.129 AC: 1968 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0651 AC: 226 AN: 3472

East Asian (EAS) AF: 0.0875 AC: 452 AN: 5168

South Asian (SAS) AF: 0.132 AC: 634 AN: 4810

European-Finnish (FIN) AF: 0.0528 AC: 557 AN: 10556

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0671 AC: 4563 AN: 67996

Other (OTH) AF: 0.130 AC: 274 AN: 2110

Alfa AF: 0.107 Hom.: 3765

Bravo AF: 0.193

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.71
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1864729; hg19: chr8-98282189;