rs2760535

Positions:

• chr1-192580782-G-A

Variant summary

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

The ENST00000644134.1(ENSG00000285280):​n.468-11478C>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 0.151 in 152,004 control chromosomes in the GnomAD database, including 2,846 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 0.15 (2846 hom., cov: 32)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593

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 (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.287+12817C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000644134.1	n.468-11478C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22957 AN: 151886 Hom.: 2841 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0762

Gnomad FIN AF: 0.0805

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.151 AC: 22987 AN: 152004 Hom.: 2846 Cov.: 32 AF XY: 0.148 AC XY: 10960 AN XY: 74298

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.0866

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0761

Gnomad4 FIN AF: 0.0805

Gnomad4 NFE AF: 0.0844

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0882 Hom.: 1610

Bravo AF: 0.160

Asia WGS AF: 0.0520 AC: 180 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	4.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2760535; hg19: chr1-192549912;