rs10801282

Positions:

• chr1-194035776-G-A
• chr1-194035776-G-C

Variant summary

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

The ENST00000656143.1(ENSG00000227240):​n.378+136409G>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 0.497 in 150,390 control chromosomes in the GnomAD database, including 20,928 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 0.50 (20928 hom., cov: 29)
• Consequence: ENST00000656143.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904475	XR_007066777.1	n.5413-90364G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656143.1	n.378+136409G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.497 AC: 74696 AN: 150316 Hom.: 20935 Cov.: 29

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.497 AC: 74691 AN: 150390 Hom.: 20928 Cov.: 29 AF XY: 0.493 AC XY: 36135 AN XY: 73350

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.540

Alfa AF: 0.541 Hom.: 4046

Bravo AF: 0.484

Asia WGS AF: 0.487 AC: 1698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10801282; hg19: chr1-194004906;