rs7225881

Variant names:

• chr17-74159163-G-A
• rs7225881
• ENST00000727556.1:n.238+17441C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-74159163-G-A
• chr17-74159163-G-T

Variant summary

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

The ENST00000727556.1(LINC02074):​n.238+17441C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,104 control chromosomes in the GnomAD database, including 3,665 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 0.21 (3665 hom., cov: 32)
• Consequence: LINC02074 ENST00000727556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 3 publications found

Genes affected

LINC02074 (HGNC:52920): (long intergenic non-protein coding RNA 2074)

ENSG00000295064 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 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
LINC02074	ENST00000727556.1	n.238+17441C>T		intron_variant	Intron 1 of 2
LINC02074	ENST00000727557.1	n.230+17441C>T		intron_variant	Intron 1 of 1
ENSG00000295064	ENST00000727722.1	n.39-3210C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32062 AN: 151986 Hom.: 3659 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.211 AC: 32090 AN: 152104 Hom.: 3665 Cov.: 32 AF XY: 0.211 AC XY: 15718 AN XY: 74354

African (AFR) AF: 0.128 AC: 5321 AN: 41494

American (AMR) AF: 0.200 AC: 3060 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3468

East Asian (EAS) AF: 0.261 AC: 1347 AN: 5166

South Asian (SAS) AF: 0.153 AC: 735 AN: 4814

European-Finnish (FIN) AF: 0.302 AC: 3197 AN: 10590

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17040 AN: 67958

Other (OTH) AF: 0.214 AC: 452 AN: 2116

Alfa AF: 0.234 Hom.: 14162

Bravo AF: 0.201

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.25
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7225881; hg19: chr17-72155302;