11-76621166-T-G

Position:

• chr11-76621166-T-G

Variant summary

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

The ENST00000637683.1(LINC02757):​n.1027+5407A>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 0.0922 in 152,172 control chromosomes in the GnomAD database, including 957 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 0.092 (957 hom., cov: 31)
• Consequence: LINC02757 ENST00000637683.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699

Genes affected

LINC02757 (HGNC:54277): (long intergenic non-protein coding RNA 2757)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02757	XR_950334.2	n.2141+5407A>C		intron_variant, non_coding_transcript_variant
LINC02757	XR_001748311.2	n.2304+4702A>C		intron_variant, non_coding_transcript_variant
LINC02757	XR_001748312.2	n.1409+4702A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02757	ENST00000637683.1	n.1027+5407A>C		intron_variant, non_coding_transcript_variant		5
LINC02757	ENST00000656117.1	n.353+7238A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0923 AC: 14035 AN: 152054 Hom.: 960 Cov.: 31

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0932

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0922 AC: 14026 AN: 152172 Hom.: 957 Cov.: 31 AF XY: 0.0974 AC XY: 7244 AN XY: 74370

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0932

Gnomad4 OTH AF: 0.0990

Alfa AF: 0.0979 Hom.: 859

Bravo AF: 0.0918

Asia WGS AF: 0.185 AC: 641 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11236809; hg19: chr11-76332210;