5-165239224-A-G

Variant names:

• chr5-165239224-A-G
• rs7720663
• ENST00000521341.1:n.420+1238T>C

Variant summary

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

The ENST00000521341.1(LINC01938):​n.420+1238T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,974 control chromosomes in the GnomAD database, including 14,848 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 0.44 (14848 hom., cov: 32)
• Consequence: LINC01938 ENST00000521341.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 3 publications found

Genes affected

LINC01938 (HGNC:52761): (long intergenic non-protein coding RNA 1938)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01938	NR_183276.1	n.695+1238T>C		intron_variant	Intron 4 of 4
LINC01938	NR_183277.1	n.696-662T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01938	ENST00000521341.1	n.420+1238T>C		intron_variant	Intron 2 of 2	2
LINC01938	ENST00000523538.2	n.1126-662T>C		intron_variant	Intron 2 of 2	3
LINC01938	ENST00000655559.1	n.903+1238T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66287 AN: 151856 Hom.: 14834 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.436 AC: 66321 AN: 151974 Hom.: 14848 Cov.: 32 AF XY: 0.444 AC XY: 32966 AN XY: 74284

African (AFR) AF: 0.469 AC: 19424 AN: 41438

American (AMR) AF: 0.520 AC: 7952 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3468

East Asian (EAS) AF: 0.590 AC: 3036 AN: 5148

South Asian (SAS) AF: 0.465 AC: 2243 AN: 4820

European-Finnish (FIN) AF: 0.491 AC: 5187 AN: 10560

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26403 AN: 67950

Other (OTH) AF: 0.393 AC: 826 AN: 2104

Alfa AF: 0.402 Hom.: 7551

Bravo AF: 0.441

Asia WGS AF: 0.498 AC: 1729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.020
DANN	Benign	0.57
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs7720663; hg19: chr5-164666230;