chr21-28410531-A-G

Variant names:

• chr21-28410531-A-G
• rs7278456
• ENST00000657148.1:n.1645+6544T>C

Variant summary

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

The ENST00000657148.1(LINC03138):​n.1645+6544T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0874 in 152,192 control chromosomes in the GnomAD database, including 771 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 0.087 (771 hom., cov: 32)
• Consequence: LINC03138 ENST00000657148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 1 publications found

Genes affected

LINC03138 (HGNC:58104):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657148.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03138	ENST00000657148.1		n.1645+6544T>C		intron	N/A
	LINC03138	ENST00000824757.1		n.769+6544T>C		intron	N/A
	LINC03138	ENST00000824758.1		n.1180+6544T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0874 AC: 13285 AN: 152074 Hom.: 768 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.0445

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0874 AC: 13296 AN: 152192 Hom.: 771 Cov.: 32 AF XY: 0.0877 AC XY: 6528 AN XY: 74406

African (AFR) AF: 0.139 AC: 5759 AN: 41490

American (AMR) AF: 0.0445 AC: 680 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3468

East Asian (EAS) AF: 0.120 AC: 624 AN: 5184

South Asian (SAS) AF: 0.223 AC: 1073 AN: 4814

European-Finnish (FIN) AF: 0.0316 AC: 335 AN: 10598

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0647 AC: 4404 AN: 68020

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0793 Hom.: 338

Bravo AF: 0.0866

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.41
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs7278456; hg19: chr21-29782852;