4-185078389-G-A

Position:

• chr4-185078389-G-A

Variant summary

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

The XR_002959837.1(LOC105377588):​n.890C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 518,070 control chromosomes in the GnomAD database, including 97,392 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 0.63 (30631 hom., cov: 33)
  • Exomes 𝑓: 0.60 (66761 hom.)
• Consequence: LOC105377588 XR_002959837.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

Genes affected

LOC105377588 (HGNC:):

LINC02436 (HGNC:53368): (long intergenic non-protein coding RNA 2436)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377588	XR_002959837.1	n.890C>T		non_coding_transcript_exon_variant	2/3
LINC02436	NR_174108.1	n.404-7395G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02436	ENST00000509017.6	n.1499+6316G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95744 AN: 152012 Hom.: 30601 Cov.: 33

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.648

GnomAD3 exomes AF: 0.589 AC: 134859 AN: 228804 Hom.: 40869 AF XY: 0.593 AC XY: 75011 AN XY: 126436

Gnomad AFR exome AF: 0.691

Gnomad AMR exome AF: 0.524

Gnomad ASJ exome AF: 0.745

Gnomad EAS exome AF: 0.333

Gnomad SAS exome AF: 0.576

Gnomad FIN exome AF: 0.566

Gnomad NFE exome AF: 0.630

Gnomad OTH exome AF: 0.613

GnomAD4 exome AF: 0.598 AC: 218973 AN: 365940 Hom.: 66761 Cov.: 0 AF XY: 0.599 AC XY: 125683 AN XY: 209812

Gnomad4 AFR exome AF: 0.693

Gnomad4 AMR exome AF: 0.521

Gnomad4 ASJ exome AF: 0.745

Gnomad4 EAS exome AF: 0.331

Gnomad4 SAS exome AF: 0.576

Gnomad4 FIN exome AF: 0.565

Gnomad4 NFE exome AF: 0.624

Gnomad4 OTH exome AF: 0.619

GnomAD4 genome AF: 0.630 AC: 95822 AN: 152130 Hom.: 30631 Cov.: 33 AF XY: 0.623 AC XY: 46319 AN XY: 74358

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.646

Alfa AF: 0.635 Hom.: 19057

Bravo AF: 0.634

Asia WGS AF: 0.477 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.45
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6841061; hg19: chr4-185999543;