rs4327597

Variant names:

• chr5-12755900-A-G
• rs4327597
• ENST00000505196.1:n.380+44601A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-12755900-A-G
• chr5-12755900-A-T

Variant summary

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

The ENST00000505196.1(LINC01194):​n.380+44601A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 152,002 control chromosomes in the GnomAD database, including 48,227 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 0.79 (48227 hom., cov: 32)
• Consequence: LINC01194 ENST00000505196.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 3 publications found

Genes affected

LINC01194 (HGNC:37171): (long intergenic non-protein coding RNA 1194)

ENSG00000309201 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01194	NR_033383.1	n.380+44601A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01194	ENST00000505196.1	n.380+44601A>G		intron_variant	Intron 3 of 3	1
LINC01194	ENST00000513051.7	n.424-3459A>G		intron_variant	Intron 3 of 3	1
LINC01194	ENST00000839367.1	n.377+44601A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120119 AN: 151886 Hom.: 48203 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.791 AC: 120190 AN: 152002 Hom.: 48227 Cov.: 32 AF XY: 0.790 AC XY: 58691 AN XY: 74324

African (AFR) AF: 0.683 AC: 28287 AN: 41402

American (AMR) AF: 0.853 AC: 13030 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2892 AN: 3472

East Asian (EAS) AF: 0.533 AC: 2749 AN: 5160

South Asian (SAS) AF: 0.753 AC: 3624 AN: 4814

European-Finnish (FIN) AF: 0.848 AC: 8978 AN: 10586

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 57958 AN: 67980

Other (OTH) AF: 0.798 AC: 1686 AN: 2112

Alfa AF: 0.829 Hom.: 16119

Bravo AF: 0.786

Asia WGS AF: 0.669 AC: 2323 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	1.5
DANN	Benign	0.47
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs4327597; hg19: chr5-12756012;