8-97271401-G-A

Variant names:

• chr8-97271401-G-A
• rs2635162
• NR_125390.1:n.471+147669C>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+147669C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,090 control chromosomes in the GnomAD database, including 4,329 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 (4329 hom., cov: 32)
• Consequence: LOC101927066 NR_125390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.29
• Publications: 6 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=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 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+147669C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26587 AN: 151972 Hom.: 4323 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.175 AC: 26617 AN: 152090 Hom.: 4329 Cov.: 32 AF XY: 0.171 AC XY: 12719 AN XY: 74362

African (AFR) AF: 0.433 AC: 17941 AN: 41404

American (AMR) AF: 0.127 AC: 1940 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0651 AC: 226 AN: 3470

East Asian (EAS) AF: 0.0875 AC: 453 AN: 5178

South Asian (SAS) AF: 0.134 AC: 644 AN: 4808

European-Finnish (FIN) AF: 0.0528 AC: 560 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0670 AC: 4558 AN: 68014

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.0856 Hom.: 238

Bravo AF: 0.192

Asia WGS AF: 0.117 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0020
DANN	Benign	0.39
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs2635162; hg19: chr8-98283629;