rs12431307

Variant names:

• chr13-80070483-G-A
• rs12431307
• ENST00000639897.1:n.189-669C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-80070483-G-A
• chr13-80070483-G-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000639897.1(ENSG00000284196):​n.189-669C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,948 control chromosomes in the GnomAD database, including 13,762 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 0.42 (13761 hom., cov: 32)
  • Exomes 𝑓: 0.36 (1 hom.)
• Consequence: ENSG00000284196 ENST00000639897.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 9 publications found

Genes affected

ENSG00000284196 (HGNC:):

LINC01080 (HGNC:49123): (long intergenic non-protein coding RNA 1080)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284196	ENST00000639897.1	n.189-669C>T		intron_variant	Intron 2 of 8	5
ENSG00000284196	ENST00000639964.1	n.186-46C>T		intron_variant	Intron 2 of 5	4
ENSG00000284196	ENST00000639965.1	n.214+2906C>T		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63146 AN: 151802 Hom.: 13757 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.431

GnomAD4 exome AF: 0.357 AC: 10 AN: 28 Hom.: 1 Cov.: 0 AF XY: 0.313 AC XY: 5 AN XY: 16

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.389 AC: 7 AN: 18

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.416 AC: 63170 AN: 151920 Hom.: 13761 Cov.: 32 AF XY: 0.420 AC XY: 31159 AN XY: 74224

African (AFR) AF: 0.303 AC: 12560 AN: 41412

American (AMR) AF: 0.530 AC: 8090 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1553 AN: 3472

East Asian (EAS) AF: 0.722 AC: 3726 AN: 5160

South Asian (SAS) AF: 0.402 AC: 1936 AN: 4812

European-Finnish (FIN) AF: 0.391 AC: 4125 AN: 10546

Middle Eastern (MID) AF: 0.369 AC: 107 AN: 290

European-Non Finnish (NFE) AF: 0.439 AC: 29824 AN: 67930

Other (OTH) AF: 0.427 AC: 900 AN: 2110

Alfa AF: 0.436 Hom.: 62943

Bravo AF: 0.425

Asia WGS AF: 0.489 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	11
DANN	Benign	0.87
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs12431307; hg19: chr13-80644618;