rs10888935

Variant names:

• chr1-55595278-T-A
• rs10888935
• ENST00000422374.1:n.158+14084T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422374.1(ENSG00000234810):​n.158+14084T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,890 control chromosomes in the GnomAD database, including 22,472 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 0.52 (22472 hom., cov: 31)
• Consequence: ENSG00000234810 ENST00000422374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705

Genes affected

ENSG00000234810 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.633 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
ENSG00000234810	ENST00000422374.1	n.158+14084T>A		intron_variant	Intron 1 of 2	2
ENSG00000234810	ENST00000634769.1	n.134+14084T>A		intron_variant	Intron 1 of 3	5
ENSG00000234810	ENST00000643167.1	n.139-19643T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79471 AN: 151772 Hom.: 22460 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.524 AC: 79518 AN: 151890 Hom.: 22472 Cov.: 31 AF XY: 0.524 AC XY: 38881 AN XY: 74206

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.542

Alfa AF: 0.566 Hom.: 3164

Bravo AF: 0.520

Asia WGS AF: 0.591 AC: 2055 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.48
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10888935; hg19: chr1-56060951;