chr21-45338851-G-C

Variant names:

• chr21-45338851-G-C
• rs957794
• ENST00000454115.8:n.3401-14514G>C

Variant summary

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

The ENST00000454115.8(LINC00205):​n.3401-14514G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,250 control chromosomes in the GnomAD database, including 1,347 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 0.13 (1347 hom., cov: 33)
  • Exomes 𝑓: 0.091 (0 hom.)
• Consequence: LINC00205 ENST00000454115.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 0 publications found

Genes affected

LINC00205 (HGNC:16420): (long intergenic non-protein coding RNA 205)

LINC00316 (HGNC:19723): (long intergenic non-protein coding RNA 316)

ENSG00000229382 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00316	NR_103811.1	n.194C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00205	ENST00000454115.8	n.3401-14514G>C		intron_variant	Intron 3 of 3	1
LINC00316	ENST00000416722.2	n.228C>G		non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC00316	ENST00000757314.1	n.108C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19137 AN: 152110 Hom.: 1330 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.124

GnomAD4 exome AF: 0.0909 AC: 2 AN: 22 Hom.: 0 Cov.: 0 AF XY: 0.111 AC XY: 2 AN XY: 18

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) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0714 AC: 1 AN: 14

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.126 AC: 19193 AN: 152228 Hom.: 1347 Cov.: 33 AF XY: 0.126 AC XY: 9390 AN XY: 74444

African (AFR) AF: 0.168 AC: 6969 AN: 41502

American (AMR) AF: 0.163 AC: 2489 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0896 AC: 311 AN: 3472

East Asian (EAS) AF: 0.0608 AC: 315 AN: 5184

South Asian (SAS) AF: 0.0794 AC: 383 AN: 4826

European-Finnish (FIN) AF: 0.120 AC: 1274 AN: 10610

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7063 AN: 68006

Other (OTH) AF: 0.123 AC: 259 AN: 2114

Alfa AF: 0.0571 Hom.: 51

Bravo AF: 0.132

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.45
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs957794; hg19: chr21-46758766;