rs6740462

chr2-65440138-C-Achr2-65440138-C-G

Variant summary

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

The ENST00000597541.6(ENSG00000234255):n.939-53G>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 0.783 in 152,410 control chromosomes in the GnomAD database, including 47,137 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 0.78 (47048 hom., cov: 32)
  • Exomes 𝑓: 0.72 (89 hom.)
• Consequence: ENST00000597541.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313

Genes affected

(HGNC:):

LINC02934 (HGNC:55913): (long intergenic non-protein coding RNA 2934)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374780	XR_007086483.1	n.939-53G>T		intron_variant, non_coding_transcript_variant
LOC105374780	XR_007086487.1	n.1547-53G>T		intron_variant, non_coding_transcript_variant
LOC105374780	XR_007086488.1	n.1715-53G>T		intron_variant, non_coding_transcript_variant
LOC105374780	XR_940187.4	n.1466-53G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000597541.6	n.939-53G>T		intron_variant, non_coding_transcript_variant		5
LINC02934	ENST00000606978.5	n.172+3256C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118972 AN: 151952 Hom.: 47001 Cov.: 32

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.800

GnomAD4 exome AF: 0.721 AC: 245 AN: 340 Hom.: 89 AF XY: 0.757 AC XY: 168 AN XY: 222

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.833

Gnomad4 EAS exome AF: 0.875

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.318

Gnomad4 NFE exome AF: 0.725

Gnomad4 OTH exome AF: 0.714

GnomAD4 genome AF: 0.783 AC: 119081 AN: 152070 Hom.: 47048 Cov.: 32 AF XY: 0.780 AC XY: 57950 AN XY: 74314

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.803

Alfa AF: 0.755 Hom.: 26081

Bravo AF: 0.799

Asia WGS AF: 0.831 AC: 2891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	5.5
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6740462; hg19: chr2-65667272;