rs7664420

Variant names:

• chr4-137050598-G-A
• rs7664420
• ENST00000505736.5:n.103+38963C>T

Variant summary

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

The ENST00000505736.5(LINC02511):​n.103+38963C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.91 in 152,194 control chromosomes in the GnomAD database, including 63,565 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 0.91 (63565 hom., cov: 32)
• Consequence: LINC02511 ENST00000505736.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 0 publications found

Genes affected

LINC02511 (HGNC:53500): (long intergenic non-protein coding RNA 2511)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02511	NR_149105.1	n.103+38963C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02511	ENST00000505736.5	n.103+38963C>T		intron_variant	Intron 2 of 3	5
LINC02511	ENST00000652184.1	n.239+38963C>T		intron_variant	Intron 4 of 5
LINC02511	ENST00000656187.1	n.148-20049C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.910 AC: 138340 AN: 152078 Hom.: 63526 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.910 AC: 138431 AN: 152194 Hom.: 63565 Cov.: 32 AF XY: 0.908 AC XY: 67562 AN XY: 74432

African (AFR) AF: 0.789 AC: 32750 AN: 41500

American (AMR) AF: 0.905 AC: 13832 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3345 AN: 3472

East Asian (EAS) AF: 0.797 AC: 4127 AN: 5178

South Asian (SAS) AF: 0.912 AC: 4394 AN: 4818

European-Finnish (FIN) AF: 0.936 AC: 9925 AN: 10608

Middle Eastern (MID) AF: 0.949 AC: 277 AN: 292

European-Non Finnish (NFE) AF: 0.984 AC: 66949 AN: 68012

Other (OTH) AF: 0.915 AC: 1933 AN: 2112

Alfa AF: 0.940 Hom.: 8545

Bravo AF: 0.901

Asia WGS AF: 0.847 AC: 2947 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.51
DANN	Benign	0.71
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs7664420; hg19: chr4-137971752;