3-13701633-G-T

Position:

• chr3-13701633-G-T

Variant summary

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

The NR_027103.1(LINC00620):​n.217+13417G>T 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 0.0489 in 152,296 control chromosomes in the GnomAD database, including 434 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 0.049 (434 hom., cov: 33)
• Consequence: LINC00620 NR_027103.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382

Genes affected

LINC00620 (HGNC:44223): (long intergenic non-protein coding RNA 620)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00620	NR_027103.1	n.217+13417G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00620	ENST00000419618.2	n.217+13417G>T		intron_variant, non_coding_transcript_variant		1
LINC00620	ENST00000438915.1	n.139-44611G>T		intron_variant, non_coding_transcript_variant		4
LINC00620	ENST00000665476.1	n.205+13417G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0487 AC: 7415 AN: 152178 Hom.: 436 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.00352

Gnomad FIN AF: 0.00584

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.00985

Gnomad OTH AF: 0.0516

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

GnomAD4 genome AF: 0.0489 AC: 7442 AN: 152296 Hom.: 434 Cov.: 33 AF XY: 0.0478 AC XY: 3560 AN XY: 74480

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.0398

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.00331

Gnomad4 FIN AF: 0.00584

Gnomad4 NFE AF: 0.00985

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0146 Hom.: 82

Bravo AF: 0.0564

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9846232; hg19: chr3-13743132;