rs6017342

Variant names:

• chr20-44436388-A-C
• rs6017342
• ENST00000637248.1:n.330T>G

Your query was ambiguous. Multiple possible variants found:

• chr20-44436388-A-C
• chr20-44436388-A-G
• chr20-44436388-A-T

Variant summary

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

The ENST00000637248.1(LINC01620):​n.330T>G 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 0.625 in 154,894 control chromosomes in the GnomAD database, including 31,089 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 0.63 (30579 hom., cov: 31)
  • Exomes 𝑓: 0.57 (510 hom.)
• Consequence: LINC01620 ENST00000637248.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 74 publications found

Genes affected

LINC01620 (HGNC:16195): (long intergenic non-protein coding RNA 1620)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01620	ENST00000637248.1	n.330T>G		non_coding_transcript_exon_variant	Exon 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94947 AN: 151834 Hom.: 30522 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.631

GnomAD4 exome AF: 0.572 AC: 1684 AN: 2942 Hom.: 510 Cov.: 0 AF XY: 0.571 AC XY: 925 AN XY: 1620

African (AFR) AF: 0.717 AC: 43 AN: 60

American (AMR) AF: 0.720 AC: 36 AN: 50

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 42 AN: 72

East Asian (EAS) AF: 0.901 AC: 254 AN: 282

South Asian (SAS) AF: 0.679 AC: 19 AN: 28

European-Finnish (FIN) AF: 0.533 AC: 193 AN: 362

Middle Eastern (MID) AF: 0.625 AC: 5 AN: 8

European-Non Finnish (NFE) AF: 0.526 AC: 1026 AN: 1950

Other (OTH) AF: 0.508 AC: 66 AN: 130

GnomAD4 genome AF: 0.626 AC: 95057 AN: 151952 Hom.: 30579 Cov.: 31 AF XY: 0.629 AC XY: 46748 AN XY: 74288

African (AFR) AF: 0.734 AC: 30408 AN: 41434

American (AMR) AF: 0.703 AC: 10736 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1928 AN: 3468

East Asian (EAS) AF: 0.892 AC: 4607 AN: 5166

South Asian (SAS) AF: 0.670 AC: 3237 AN: 4830

European-Finnish (FIN) AF: 0.554 AC: 5842 AN: 10554

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36171 AN: 67918

Other (OTH) AF: 0.637 AC: 1344 AN: 2110

Alfa AF: 0.573 Hom.: 100727

Bravo AF: 0.643

Asia WGS AF: 0.821 AC: 2853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs6017342; hg19: chr20-43065028;