rs61457372

Variant names:

• chr17-72363633-T-C
• rs61457372
• ENST00000581801.7:n.658-40313A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000581801.7(LINC00511):​n.658-40313A>G variant causes a intron 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 ENST00000581801.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581801.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00511	ENST00000581801.7	TSL:3	n.658-40313A>G		intron	N/A
	LINC00511	ENST00000648088.1		n.491-40313A>G		intron	N/A
	LINC00511	ENST00000648248.1		n.394+64603A>G		intron	N/A

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

African (AFR) AF: 0.515 AC: 21213 AN: 41228

American (AMR) AF: 0.472 AC: 7184 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2153 AN: 3466

East Asian (EAS) AF: 0.728 AC: 3718 AN: 5104

South Asian (SAS) AF: 0.695 AC: 3322 AN: 4778

European-Finnish (FIN) AF: 0.688 AC: 7228 AN: 10502

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.681 AC: 46223 AN: 67864

Other (OTH) AF: 0.619 AC: 1303 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.73
PhyloP100		0.23

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs61457372;

hg19: chr17-70359774;