4-82613701-T-C

Position:

• chr4-82613701-T-C

Variant summary

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

The NR_024088.1(LINC00575):​n.576+171A>G 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 0.309 in 152,066 control chromosomes in the GnomAD database, including 7,431 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 0.31 (7431 hom., cov: 32)
• Consequence: LINC00575 NR_024088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

LINC00575 (HGNC:21342): (long intergenic non-protein coding RNA 575)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00575	NR_024088.1	n.576+171A>G		intron_variant, non_coding_transcript_variant
LINC00575	NR_024087.1	n.638+171A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00575	ENST00000426551.5	n.638+171A>G		intron_variant, non_coding_transcript_variant		1
LINC00575	ENST00000515811.1	n.576+171A>G		intron_variant, non_coding_transcript_variant		1
LINC00575	ENST00000651054.1	n.749+171A>G		intron_variant, non_coding_transcript_variant
	ENST00000667708.1	n.53-703T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46951 AN: 151946 Hom.: 7426 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.309 AC: 46983 AN: 152066 Hom.: 7431 Cov.: 32 AF XY: 0.313 AC XY: 23248 AN XY: 74312

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.304

Alfa AF: 0.302 Hom.: 7048

Bravo AF: 0.301

Asia WGS AF: 0.304 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.79
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6845080; hg19: chr4-83534854;