21-28137610-A-C

Variant names:

• chr21-28137610-A-C
• rs1571671
• ENST00000453420.5:n.706-17736T>G

Variant summary

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

The ENST00000426534.2(LINC01697):​n.1763A>C variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,950 control chromosomes in the GnomAD database, including 22,787 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 0.54 (22787 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01697 ENST00000426534.2 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.40
• Publications: 5 publications found

Genes affected

LINC01695 (HGNC:52483): (long intergenic non-protein coding RNA 1695)

LINC01697 (HGNC:52485): (long intergenic non-protein coding RNA 1697)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426534.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01695	NR_126012.1		n.706-17736T>G		intron	N/A
	LINC01697	NR_126010.1		n.*1A>C		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01695	ENST00000453420.5	TSL:1	n.706-17736T>G		intron	N/A
	LINC01697	ENST00000426534.2	TSL:2	n.1763A>C		splice_region non_coding_transcript_exon	Exon 5 of 5
	LINC01695	ENST00000737222.1		n.192-13756T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81943 AN: 151832 Hom.: 22739 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.508

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.540 AC: 82051 AN: 151950 Hom.: 22787 Cov.: 32 AF XY: 0.536 AC XY: 39784 AN XY: 74244

African (AFR) AF: 0.662 AC: 27453 AN: 41458

American (AMR) AF: 0.568 AC: 8664 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2017 AN: 3468

East Asian (EAS) AF: 0.340 AC: 1761 AN: 5176

South Asian (SAS) AF: 0.520 AC: 2502 AN: 4816

European-Finnish (FIN) AF: 0.433 AC: 4558 AN: 10528

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33467 AN: 67926

Other (OTH) AF: 0.513 AC: 1083 AN: 2112

Alfa AF: 0.542 Hom.: 3691

Bravo AF: 0.554

Asia WGS AF: 0.448 AC: 1550 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.72
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs1571671; hg19: chr21-29509929;