rs1919811

Variant names:

• chr7-53811760-C-A
• rs1919811
• ENST00000380970.2:n.172G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-53811760-C-A
• chr7-53811760-C-G

Variant summary

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

The ENST00000380970.2(LINC01446):​n.172G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,806 control chromosomes in the GnomAD database, including 23,494 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 0.55 (23386 hom., cov: 32)
  • Exomes 𝑓: 0.49 (108 hom.)
• Consequence: LINC01446 ENST00000380970.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 7 publications found

Genes affected

LINC01446 (HGNC:50773): (long intergenic non-protein coding RNA 1446)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01446	NR_038371.1	n.172G>T		non_coding_transcript_exon_variant	Exon 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01446	ENST00000380970.2	n.172G>T		non_coding_transcript_exon_variant	Exon 1 of 6	2
LINC01446	ENST00000650830.1	n.183G>T		non_coding_transcript_exon_variant	Exon 1 of 6
LINC01446	ENST00000651506.1	n.183G>T		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83285 AN: 151892 Hom.: 23356 Cov.: 32

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 0.494 AC: 393 AN: 796 Hom.: 108 Cov.: 0 AF XY: 0.528 AC XY: 279 AN XY: 528

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AF: 0.750 AC: 3 AN: 4

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.500 AC: 4 AN: 8

South Asian (SAS) AF: 0.700 AC: 7 AN: 10

European-Finnish (FIN) AF: 0.498 AC: 208 AN: 418

Middle Eastern (MID) AF: 0.500 AC: 2 AN: 4

European-Non Finnish (NFE) AF: 0.476 AC: 160 AN: 336

Other (OTH) AF: 0.300 AC: 3 AN: 10

GnomAD4 genome AF: 0.548 AC: 83368 AN: 152010 Hom.: 23386 Cov.: 32 AF XY: 0.551 AC XY: 40906 AN XY: 74296

African (AFR) AF: 0.666 AC: 27644 AN: 41488

American (AMR) AF: 0.528 AC: 8069 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1723 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3089 AN: 5132

South Asian (SAS) AF: 0.483 AC: 2329 AN: 4822

European-Finnish (FIN) AF: 0.526 AC: 5561 AN: 10570

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 32995 AN: 67944

Other (OTH) AF: 0.564 AC: 1192 AN: 2112

Alfa AF: 0.493 Hom.: 4523

Bravo AF: 0.557

Asia WGS AF: 0.547 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.39
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1919811; hg19: chr7-53879453;