rs2760524

chr1-192561418-A-Gchr1-192561418-A-T

Variant summary

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

The ENST00000644134.1(ENSG00000285280):n.595+5729T>C 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 0.861 in 152,146 control chromosomes in the GnomAD database, including 56,658 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 0.86 (56658 hom., cov: 31)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371664	XR_002958418.2	n.357+5729T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000644134.1	n.595+5729T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130821 AN: 152028 Hom.: 56598 Cov.: 31

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.861 AC: 130937 AN: 152146 Hom.: 56658 Cov.: 31 AF XY: 0.863 AC XY: 64174 AN XY: 74380

Gnomad4 AFR AF: 0.951

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.841

Alfa AF: 0.845 Hom.: 9825

Bravo AF: 0.860

Asia WGS AF: 0.872 AC: 3034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.25
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2760524; hg19: chr1-192530548;