chr5-7169777-G-A

Position:

• chr5-7169777-G-A

Variant summary

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

The ENST00000648809.1(LINC02196):​n.720-9215G>A 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 0.283 in 152,006 control chromosomes in the GnomAD database, including 7,538 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 0.28 (7538 hom., cov: 32)
• Consequence: LINC02196 ENST00000648809.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

Genes affected

LINC02196 (HGNC:53062): (long intergenic non-protein coding RNA 2196)

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 (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02196	ENST00000648809.1	n.720-9215G>A		intron_variant, non_coding_transcript_variant
LINC02196	ENST00000512838.2	n.427-9215G>A		intron_variant, non_coding_transcript_variant		4
LINC02196	ENST00000651243.2	n.380-9215G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43051 AN: 151886 Hom.: 7539 Cov.: 32

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.283 AC: 43055 AN: 152006 Hom.: 7538 Cov.: 32 AF XY: 0.285 AC XY: 21197 AN XY: 74302

Gnomad4 AFR AF: 0.0785

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.297

Alfa AF: 0.336 Hom.: 1893

Bravo AF: 0.274

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7727540; hg19: chr5-7169890;