rs10801156

Positions:

• chr1-192817254-A-C

Variant summary

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

The ENST00000644134.1(ENSG00000285280):​n.105-51060T>G 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 0.283 in 151,884 control chromosomes in the GnomAD database, including 6,282 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 0.28 (6282 hom., cov: 32)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 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.105-51060T>G		intron_variant, non_coding_transcript_variant
	ENST00000644058.1	n.194-51060T>G		intron_variant, non_coding_transcript_variant
	ENST00000645822.1	n.199+9650T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43040 AN: 151764 Hom.: 6278 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.283 AC: 43048 AN: 151884 Hom.: 6282 Cov.: 32 AF XY: 0.285 AC XY: 21181 AN XY: 74206

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.282

Alfa AF: 0.267 Hom.: 810

Bravo AF: 0.288

Asia WGS AF: 0.414 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.83
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10801156; hg19: chr1-192786384;