rs16895513

Variant names:

• chr8-97314745-C-T
• rs16895513
• NR_125390.1:n.471+104325G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_125390.1(LOC101927066):​n.471+104325G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,152 control chromosomes in the GnomAD database, including 7,580 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 (7580 hom., cov: 33)
• Consequence: LOC101927066 NR_125390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 3 publications found

Genes affected

LOC101927066 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927066	NR_125390.1	n.471+104325G>A		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46394 AN: 152034 Hom.: 7572 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.327

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: 46441 AN: 152152 Hom.: 7580 Cov.: 33 AF XY: 0.300 AC XY: 22302 AN XY: 74388

African (AFR) AF: 0.386 AC: 16028 AN: 41504

American (AMR) AF: 0.227 AC: 3471 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3466

East Asian (EAS) AF: 0.0200 AC: 104 AN: 5190

South Asian (SAS) AF: 0.161 AC: 775 AN: 4820

European-Finnish (FIN) AF: 0.327 AC: 3459 AN: 10576

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20681 AN: 67994

Other (OTH) AF: 0.283 AC: 599 AN: 2114

Alfa AF: 0.296 Hom.: 1231

Bravo AF: 0.300

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	16
DANN	Benign	0.65
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs16895513; hg19: chr8-98326973;