21-27100170-A-G

Variant names:

• chr21-27100170-A-G
• rs10482982
• ENST00000743056.1:n.346+25337A>G

Variant summary

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

The ENST00000743056.1(ENSG00000296857):​n.346+25337A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0571 in 152,334 control chromosomes in the GnomAD database, including 322 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 0.057 (322 hom., cov: 33)
• Consequence: ENSG00000296857 ENST00000743056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 1 publications found

Genes affected

ENSG00000296857 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743056.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296857	ENST00000743056.1		n.346+25337A>G		intron	N/A
	ENSG00000296857	ENST00000743057.1		n.269+25337A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0571 AC: 8691 AN: 152216 Hom.: 320 Cov.: 33

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0559

Gnomad ASJ AF: 0.0498

Gnomad EAS AF: 0.00288

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0816

Gnomad OTH AF: 0.0607

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

GnomAD4 genome AF: 0.0571 AC: 8698 AN: 152334 Hom.: 322 Cov.: 33 AF XY: 0.0569 AC XY: 4241 AN XY: 74500

African (AFR) AF: 0.0166 AC: 689 AN: 41572

American (AMR) AF: 0.0559 AC: 855 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0498 AC: 173 AN: 3472

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5192

South Asian (SAS) AF: 0.113 AC: 547 AN: 4826

European-Finnish (FIN) AF: 0.0603 AC: 640 AN: 10622

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0816 AC: 5550 AN: 68028

Other (OTH) AF: 0.0639 AC: 135 AN: 2114

Alfa AF: 0.0710 Hom.: 711

Bravo AF: 0.0514

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.76
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10482982; hg19: chr21-28472489;