rs2197879

Variant names:

• chr13-38671051-A-T
• rs2197879
• ENST00000756067.1:n.587+12636T>A

Variant summary

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

The ENST00000756067.1(LINC00437):​n.587+12636T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,108 control chromosomes in the GnomAD database, including 17,454 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 0.43 (17454 hom., cov: 33)
• Consequence: LINC00437 ENST00000756067.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 2 publications found

Genes affected

LINC00437 (HGNC:42772): (long intergenic non-protein coding RNA 437)

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 (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00437	NR_126377.1	n.338+12636T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00437	ENST00000756067.1	n.587+12636T>A		intron_variant	Intron 2 of 2
LINC00437	ENST00000756068.1	n.486+15388T>A		intron_variant	Intron 1 of 1
LINC00437	ENST00000756069.1	n.586+12636T>A		intron_variant	Intron 2 of 3
LINC00437	ENST00000756070.1	n.412+15388T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64943 AN: 151990 Hom.: 17401 Cov.: 33

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.428 AC: 65057 AN: 152108 Hom.: 17454 Cov.: 33 AF XY: 0.426 AC XY: 31708 AN XY: 74346

African (AFR) AF: 0.767 AC: 31816 AN: 41496

American (AMR) AF: 0.421 AC: 6433 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1066 AN: 3468

East Asian (EAS) AF: 0.367 AC: 1898 AN: 5178

South Asian (SAS) AF: 0.294 AC: 1417 AN: 4820

European-Finnish (FIN) AF: 0.316 AC: 3336 AN: 10566

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17950 AN: 67986

Other (OTH) AF: 0.376 AC: 794 AN: 2112

Alfa AF: 0.357 Hom.: 1491

Bravo AF: 0.449

Asia WGS AF: 0.376 AC: 1307 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	1.3
DANN	Benign	0.82
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2197879; hg19: chr13-39245188;