rs2421141

Variant names:

• chr10-122890920-A-G
• rs2421141
• ENST00000368895.2:n.1096+2197A>G

Variant summary

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

The ENST00000425266.4(ENSG00000293310):​n.880+2197A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,970 control chromosomes in the GnomAD database, including 17,823 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 0.47 (17823 hom., cov: 32)
• Consequence: ENSG00000293310 ENST00000425266.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 3 publications found

Genes affected

C10orf88B (HGNC:44080): (C10orf88B (pseudogene))

ENSG00000293310 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425266.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf88B	NR_027282.1		n.1190+2197A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf88B	ENST00000368895.2	TSL:6	n.1096+2197A>G		intron	N/A
	ENSG00000293310	ENST00000425266.4	TSL:2	n.880+2197A>G		intron	N/A
	ENSG00000293310	ENST00000750902.1		n.979+2197A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71997 AN: 151852 Hom.: 17824 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.474 AC: 72013 AN: 151970 Hom.: 17823 Cov.: 32 AF XY: 0.476 AC XY: 35355 AN XY: 74290

African (AFR) AF: 0.341 AC: 14123 AN: 41464

American (AMR) AF: 0.467 AC: 7133 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3468

East Asian (EAS) AF: 0.425 AC: 2196 AN: 5168

South Asian (SAS) AF: 0.459 AC: 2210 AN: 4818

European-Finnish (FIN) AF: 0.622 AC: 6555 AN: 10534

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36268 AN: 67920

Other (OTH) AF: 0.488 AC: 1032 AN: 2116

Alfa AF: 0.494 Hom.: 2379

Bravo AF: 0.455

Asia WGS AF: 0.434 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2421141;

hg19: chr10-124650436;