chr20-7156675-T-C

Position:

• chr20-7156675-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000449581.1(LINC01428):​n.299-8476A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0161 in 152,338 control chromosomes in the GnomAD database, including 28 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 0.016 (28 hom., cov: 32)
• Consequence: LINC01428 ENST00000449581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

Genes affected

LINC01428 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0161 (2452/152338) while in subpopulation EAS AF= 0.0451 (234/5190). AF 95% confidence interval is 0.0404. There are 28 homozygotes in gnomad4. There are 1236 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 28 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01428	NR_110609.1	n.299-8476A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01428	ENST00000449581.1	n.299-8476A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0161 AC: 2456 AN: 152220 Hom.: 28 Cov.: 32

Gnomad AFR AF: 0.00972

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0206

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.0454

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.00960

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0168

Gnomad OTH AF: 0.0263

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

GnomAD4 genome AF: 0.0161 AC: 2452 AN: 152338 Hom.: 28 Cov.: 32 AF XY: 0.0166 AC XY: 1236 AN XY: 74508

Gnomad4 AFR AF: 0.00972

Gnomad4 AMR AF: 0.0206

Gnomad4 ASJ AF: 0.0153

Gnomad4 EAS AF: 0.0451

Gnomad4 SAS AF: 0.0292

Gnomad4 FIN AF: 0.00960

Gnomad4 NFE AF: 0.0168

Gnomad4 OTH AF: 0.0260

Alfa AF: 0.0154 Hom.: 8

Bravo AF: 0.0165

Asia WGS AF: 0.0340 AC: 118 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	1.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485714; hg19: chr20-7137322;