rs2388121

Variant names:

• chr10-2062221-G-A
• rs2388121
• ENST00000690470.2:n.117-2704C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-2062221-G-A
• chr10-2062221-G-C
• chr10-2062221-G-T

Variant summary

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

The ENST00000690470.2(ENSG00000289427):​n.117-2704C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,972 control chromosomes in the GnomAD database, including 29,776 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 0.62 (29776 hom., cov: 31)
• Consequence: ENSG00000289427 ENST00000690470.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.955
• Publications: 1 publications found

Genes affected

ENSG00000289427 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289427	ENST00000690470.2	n.117-2704C>T		intron_variant	Intron 1 of 2
ENSG00000289427	ENST00000846787.1	n.43+8042C>T		intron_variant	Intron 1 of 3
ENSG00000289427	ENST00000846788.1	n.116+8042C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94236 AN: 151854 Hom.: 29713 Cov.: 31

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.621 AC: 94366 AN: 151972 Hom.: 29776 Cov.: 31 AF XY: 0.614 AC XY: 45611 AN XY: 74268

African (AFR) AF: 0.737 AC: 30574 AN: 41468

American (AMR) AF: 0.630 AC: 9610 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2001 AN: 3466

East Asian (EAS) AF: 0.571 AC: 2942 AN: 5154

South Asian (SAS) AF: 0.567 AC: 2727 AN: 4810

European-Finnish (FIN) AF: 0.487 AC: 5131 AN: 10542

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39500 AN: 67970

Other (OTH) AF: 0.598 AC: 1258 AN: 2102

Alfa AF: 0.592 Hom.: 111896

Bravo AF: 0.634

Asia WGS AF: 0.598 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.68
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs2388121; hg19: chr10-2104415;