rs10801153

Positions:

• chr1-192794818-G-A
• chr1-192794818-G-C
• chr1-192794818-G-T

Variant summary

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

The ENST00000644134.1(ENSG00000285280):​n.105-28624C>T 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 0.271 in 152,056 control chromosomes in the GnomAD database, including 5,764 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 0.27 (5764 hom., cov: 32)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000644134.1	n.105-28624C>T		intron_variant, non_coding_transcript_variant
	ENST00000644058.1	n.194-28624C>T		intron_variant, non_coding_transcript_variant
	ENST00000645822.1	n.200-2350C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41264 AN: 151936 Hom.: 5763 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.271 AC: 41265 AN: 152056 Hom.: 5764 Cov.: 32 AF XY: 0.271 AC XY: 20165 AN XY: 74330

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.267

Alfa AF: 0.283 Hom.: 9843

Bravo AF: 0.267

Asia WGS AF: 0.393 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10801153; hg19: chr1-192763948;