11-44693132-C-G

Position:

• chr11-44693132-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_931234.3(LINC02704):​n.196+3089G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,678 control chromosomes in the GnomAD database, including 18,961 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 0.46 (18961 hom., cov: 32)
• Consequence: LINC02704 XR_931234.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

Genes affected

LINC02704 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02704	XR_931234.3	n.196+3089G>C		intron_variant, non_coding_transcript_variant
LINC02704	XR_007062658.1	n.359+1723G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69198 AN: 151558 Hom.: 18969 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.456 AC: 69165 AN: 151678 Hom.: 18961 Cov.: 32 AF XY: 0.451 AC XY: 33444 AN XY: 74096

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.466

Alfa AF: 0.415 Hom.: 1413

Bravo AF: 0.427

Asia WGS AF: 0.310 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7115456; hg19: chr11-44714682;