3-150337774-G-T

Variant names:

• chr3-150337774-G-T
• rs1597466
• ENST00000716187.1:n.623+3332C>A

Variant summary

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

The ENST00000716187.1(LINC01214):​n.623+3332C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 151,820 control chromosomes in the GnomAD database, including 3,081 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 0.16 (3081 hom., cov: 32)
• Consequence: LINC01214 ENST00000716187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 13 publications found

Genes affected

LINC01214 (HGNC:49650): (long intergenic non-protein coding RNA 1214)

ENSG00000297695 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986141	XR_001740958.1	n.1982-9604G>T		intron_variant	Intron 1 of 2
LOC107986141	XR_007096127.1	n.1982-9604G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01214	ENST00000716187.1	n.623+3332C>A		intron_variant	Intron 2 of 3
LINC01214	ENST00000716189.1	n.710+3332C>A		intron_variant	Intron 5 of 5
LINC01214	ENST00000749916.1	n.798+3332C>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24349 AN: 151702 Hom.: 3062 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.0941

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.161 AC: 24411 AN: 151820 Hom.: 3081 Cov.: 32 AF XY: 0.156 AC XY: 11554 AN XY: 74218

African (AFR) AF: 0.354 AC: 14628 AN: 41364

American (AMR) AF: 0.0947 AC: 1447 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0814 AC: 392 AN: 4816

European-Finnish (FIN) AF: 0.0659 AC: 690 AN: 10478

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.0941 AC: 6392 AN: 67924

Other (OTH) AF: 0.150 AC: 315 AN: 2104

Alfa AF: 0.0861 Hom.: 331

Bravo AF: 0.172

Asia WGS AF: 0.0600 AC: 208 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.5
DANN	Benign	0.63
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1597466; hg19: chr3-150055561;