rs4681577

Variant names:

• chr3-150116202-G-A
• rs4681577
• ENST00000472821.6:n.161-8736G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-150116202-G-A
• chr3-150116202-G-C
• chr3-150116202-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000472821.6(LINC01213):​n.161-8736G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000572 in 152,082 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00057 (0 hom., cov: 30)
• Consequence: LINC01213 ENST00000472821.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 1 publications found

Genes affected

LINC01213 (HGNC:49648): (long intergenic non-protein coding RNA 1213)

LOC105374313 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374313	NR_136187.1	n.156-8736G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01213	ENST00000472821.6	n.161-8736G>A		intron_variant	Intron 1 of 2	3
LINC01213	ENST00000487840.6	n.99-8736G>A		intron_variant	Intron 1 of 2	2
LINC01213	ENST00000489690.1	n.120-8736G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.000559 AC: 85 AN: 151962 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00172

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00144

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

GnomAD4 genome AF: 0.000572 AC: 87 AN: 152082 Hom.: 0 Cov.: 30 AF XY: 0.000565 AC XY: 42 AN XY: 74364

African (AFR) AF: 0.00176 AC: 73 AN: 41446

American (AMR) AF: 0.000655 AC: 10 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5160

South Asian (SAS) AF: 0.00 AC: 0 AN: 4808

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10588

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68014

Other (OTH) AF: 0.00142 AC: 3 AN: 2112

Alfa AF: 0.00 Hom.: 17089

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.90
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4681577; hg19: chr3-149833989;