21-44842776-T-A

Variant names:

• chr21-44842776-T-A
• rs2838702
• ENST00000816895.1:n.350+70A>T

Variant summary

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

The ENST00000816895.1(ENSG00000306307):​n.350+70A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,974 control chromosomes in the GnomAD database, including 9,243 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 0.34 (9243 hom., cov: 31)
• Consequence: ENSG00000306307 ENST00000816895.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 3 publications found

Genes affected

ENSG00000306307 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816895.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306307	ENST00000816895.1		n.350+70A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51675 AN: 151856 Hom.: 9232 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.340 AC: 51714 AN: 151974 Hom.: 9243 Cov.: 31 AF XY: 0.346 AC XY: 25704 AN XY: 74288

African (AFR) AF: 0.256 AC: 10612 AN: 41464

American (AMR) AF: 0.384 AC: 5875 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1187 AN: 3468

East Asian (EAS) AF: 0.596 AC: 3075 AN: 5158

South Asian (SAS) AF: 0.384 AC: 1849 AN: 4820

European-Finnish (FIN) AF: 0.432 AC: 4553 AN: 10544

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23593 AN: 67930

Other (OTH) AF: 0.336 AC: 708 AN: 2108

Alfa AF: 0.338 Hom.: 1085

Bravo AF: 0.340

Asia WGS AF: 0.450 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.64
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2838702; hg19: chr21-46262691;