rs2772577

chr9-24547234-G-A

Variant summary

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

The ENST00000649380.1(ENSG00000269957):n.192+1105G>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 0.182 in 152,084 control chromosomes in the GnomAD database, including 2,892 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 0.18 (2892 hom., cov: 32)
• Consequence: ENST00000649380.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

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 (NFE) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649380.1	n.192+1105G>A		intron_variant, non_coding_transcript_variant
	ENST00000602614.1	n.132+1105G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000602851.5	n.178+1105G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27638 AN: 151966 Hom.: 2890 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.182 AC: 27648 AN: 152084 Hom.: 2892 Cov.: 32 AF XY: 0.179 AC XY: 13325 AN XY: 74326

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0497

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.182

Alfa AF: 0.206 Hom.: 973

Bravo AF: 0.170

Asia WGS AF: 0.105 AC: 364 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	3.5
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2772577; hg19: chr9-24547232;