rs10484174

Variant names:

• chr14-44639920-G-A
• rs10484174
• ENST00000795537.1:n.153+8925C>T

Variant summary

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

The ENST00000795537.1(LINC02277):​n.153+8925C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,000 control chromosomes in the GnomAD database, including 5,534 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 0.26 (5534 hom., cov: 32)
• Consequence: LINC02277 ENST00000795537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 0 publications found

Genes affected

LINC02277 (HGNC:53193): (long intergenic non-protein coding RNA 2277)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02277	ENST00000795537.1	n.153+8925C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39708 AN: 151882 Hom.: 5521 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.262 AC: 39755 AN: 152000 Hom.: 5534 Cov.: 32 AF XY: 0.264 AC XY: 19609 AN XY: 74320

African (AFR) AF: 0.288 AC: 11928 AN: 41472

American (AMR) AF: 0.170 AC: 2590 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3464

East Asian (EAS) AF: 0.0774 AC: 401 AN: 5180

South Asian (SAS) AF: 0.252 AC: 1215 AN: 4828

European-Finnish (FIN) AF: 0.372 AC: 3927 AN: 10566

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18376 AN: 67932

Other (OTH) AF: 0.232 AC: 489 AN: 2110

Alfa AF: 0.263 Hom.: 10539

Bravo AF: 0.245

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.66
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10484174; hg19: chr14-45109123;