rs10021288

Variant names:

• chr4-122084379-G-A
• rs10021288
• ENST00000777386.1:n.121-1113G>A

Variant summary

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

The ENST00000777386.1(ENSG00000301253):​n.121-1113G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,200 control chromosomes in the GnomAD database, including 3,568 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 0.21 (3568 hom., cov: 32)
• Consequence: ENSG00000301253 ENST00000777386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 9 publications found

Genes affected

ENSG00000301253 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777386.1. 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
	ENSG00000301253	ENST00000777386.1		n.121-1113G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31445 AN: 152078 Hom.: 3568 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.207 AC: 31442 AN: 152200 Hom.: 3568 Cov.: 32 AF XY: 0.207 AC XY: 15395 AN XY: 74410

African (AFR) AF: 0.131 AC: 5437 AN: 41554

American (AMR) AF: 0.160 AC: 2450 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 869 AN: 3468

East Asian (EAS) AF: 0.107 AC: 557 AN: 5186

South Asian (SAS) AF: 0.149 AC: 719 AN: 4826

European-Finnish (FIN) AF: 0.314 AC: 3329 AN: 10586

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17457 AN: 67974

Other (OTH) AF: 0.193 AC: 409 AN: 2114

Alfa AF: 0.214 Hom.: 960

Bravo AF: 0.190

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.34
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10021288; hg19: chr4-123005534;