ENST00000416641.2:n.210+7081G>T

Variant names:

• chr21-17667969-C-A
• rs10482889
• ENST00000416641.2:n.210+7081G>T

Variant summary

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

The ENST00000416641.2(ENSG00000226956):​n.210+7081G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0934 in 152,152 control chromosomes in the GnomAD database, including 1,888 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 0.093 (1888 hom., cov: 32)
• Consequence: ENSG00000226956 ENST00000416641.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 1 publications found

Genes affected

ENSG00000226956 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904999	XR_007067821.1	n.64+6387G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226956	ENST00000416641.2	n.210+7081G>T		intron_variant	Intron 1 of 2	3
ENSG00000226956	ENST00000813567.1	n.339-8300G>T		intron_variant	Intron 1 of 1
ENSG00000226956	ENST00000813569.1	n.222+7081G>T		intron_variant	Intron 1 of 1
ENSG00000226956	ENST00000813570.1	n.100+2798G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0933 AC: 14179 AN: 152034 Hom.: 1881 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0485

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0678

Gnomad FIN AF: 0.00302

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00738

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0934 AC: 14211 AN: 152152 Hom.: 1888 Cov.: 32 AF XY: 0.0918 AC XY: 6831 AN XY: 74414

African (AFR) AF: 0.289 AC: 11975 AN: 41454

American (AMR) AF: 0.0483 AC: 739 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3470

East Asian (EAS) AF: 0.0249 AC: 129 AN: 5184

South Asian (SAS) AF: 0.0666 AC: 321 AN: 4818

European-Finnish (FIN) AF: 0.00302 AC: 32 AN: 10608

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.00737 AC: 501 AN: 68008

Other (OTH) AF: 0.0767 AC: 162 AN: 2112

Alfa AF: 0.0329 Hom.: 255

Bravo AF: 0.105

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10482889; hg19: chr21-19040287;