rs10888935

chr1-55595278-T-A

Variant summary

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

The ENST00000643167.1(ENSG00000234810):n.139-19643T>A variant causes a intron, non coding transcript 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: ENST00000643167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000643167.1	n.139-19643T>A		intron_variant, non_coding_transcript_variant

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;