rs2995271

Variant names:

• chr10-30230903-C-T
• rs2995271
• NR_120653.1:n.269-14C>T

Variant summary

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

The NR_120653.1(LOC101929279):​n.269-14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,022 control chromosomes in the GnomAD database, including 33,695 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 0.64 (33695 hom., cov: 31)
• Consequence: LOC101929279 NR_120653.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 13 publications found

Genes affected

LOC101929279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_120653.1. 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
	LOC101929279	NR_120653.1		n.269-14C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97631 AN: 151904 Hom.: 33684 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.642 AC: 97671 AN: 152022 Hom.: 33695 Cov.: 31 AF XY: 0.643 AC XY: 47772 AN XY: 74280

African (AFR) AF: 0.403 AC: 16696 AN: 41412

American (AMR) AF: 0.689 AC: 10529 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2493 AN: 3472

East Asian (EAS) AF: 0.281 AC: 1450 AN: 5166

South Asian (SAS) AF: 0.625 AC: 3009 AN: 4818

European-Finnish (FIN) AF: 0.802 AC: 8473 AN: 10568

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52720 AN: 67998

Other (OTH) AF: 0.650 AC: 1371 AN: 2108

Alfa AF: 0.722 Hom.: 93568

Bravo AF: 0.621

Asia WGS AF: 0.437 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	8.1
DANN	Benign	0.89
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2995271; hg19: chr10-30519832;