rs61457372

Positions:

• chr17-72363633-T-C
• chr17-72363633-T-G

Variant summary

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

The ENST00000648631.1(LINC00511):​n.1470+19410A>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 0.615 in 151,476 control chromosomes in the GnomAD database, including 29,221 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 0.62 (29221 hom., cov: 29)
• Consequence: LINC00511 ENST00000648631.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

Genes affected

LINC00511 (HGNC:43564): (long intergenic non-protein coding RNA 511)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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
LINC00511	ENST00000648631.1	n.1470+19410A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93123 AN: 151356 Hom.: 29215 Cov.: 29

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.615 AC: 93163 AN: 151476 Hom.: 29221 Cov.: 29 AF XY: 0.614 AC XY: 45411 AN XY: 73990

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.619

Alfa AF: 0.648 Hom.: 4963

Bravo AF: 0.594

Asia WGS AF: 0.704 AC: 2451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61457372; hg19: chr17-70359774;