14-21203118-G-T

Variant names:

• chr14-21203118-G-T
• rs10483251
• ENST00000555688.1:n.291-1185C>A

Variant summary

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

The ENST00000555688.1(LINC00641):​n.291-1185C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,122 control chromosomes in the GnomAD database, including 3,904 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 0.21 (3904 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC00641 ENST00000555688.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580
• Publications: 9 publications found

Genes affected

LINC00641 (HGNC:27511): (long intergenic non-protein coding RNA 641)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00641	NR_038970.1	n.2386C>A		non_coding_transcript_exon_variant	Exon 1 of 1
LINC00641	NR_038971.1	n.291-1185C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00641	ENST00000555688.1	n.291-1185C>A		intron_variant	Intron 1 of 1	1
LINC00641	ENST00000555379.1	n.2386C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31412 AN: 152006 Hom.: 3895 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0801

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.207

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

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: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.207 AC: 31441 AN: 152122 Hom.: 3904 Cov.: 32 AF XY: 0.211 AC XY: 15665 AN XY: 74360

African (AFR) AF: 0.120 AC: 4963 AN: 41504

American (AMR) AF: 0.387 AC: 5906 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 526 AN: 3468

East Asian (EAS) AF: 0.0805 AC: 417 AN: 5180

South Asian (SAS) AF: 0.240 AC: 1160 AN: 4824

European-Finnish (FIN) AF: 0.235 AC: 2485 AN: 10586

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15245 AN: 67978

Other (OTH) AF: 0.207 AC: 437 AN: 2108

Alfa AF: 0.213 Hom.: 6009

Bravo AF: 0.215

Asia WGS AF: 0.189 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.8
DANN	Benign	0.73
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs10483251; hg19: chr14-21671277;