NR_157978.1:n.510G>A

Variant names:

• chr2-20488758-C-T
• rs13021401
• NR_157978.1:n.510G>A

Variant summary

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

The NR_157978.1(LOC107985856):​n.510G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,192 control chromosomes in the GnomAD database, including 5,141 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 0.24 (5141 hom., cov: 33)
• Consequence: LOC107985856 NR_157978.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21
• Publications: 19 publications found

Genes affected

LOC107985856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985856	NR_157978.1	n.510G>A		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228950	ENST00000448241.2	n.309-9026C>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36118 AN: 152074 Hom.: 5127 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.238 AC: 36149 AN: 152192 Hom.: 5141 Cov.: 33 AF XY: 0.241 AC XY: 17958 AN XY: 74392

African (AFR) AF: 0.124 AC: 5138 AN: 41532

American (AMR) AF: 0.283 AC: 4333 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3466

East Asian (EAS) AF: 0.633 AC: 3280 AN: 5184

South Asian (SAS) AF: 0.447 AC: 2152 AN: 4814

European-Finnish (FIN) AF: 0.204 AC: 2163 AN: 10588

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17450 AN: 67992

Other (OTH) AF: 0.232 AC: 491 AN: 2112

Alfa AF: 0.265 Hom.: 18958

Bravo AF: 0.238

Asia WGS AF: 0.492 AC: 1711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.5
DANN	Benign	0.44
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs13021401; hg19: chr2-20688519;