rs2772577

Variant names:

• chr9-24547234-G-A
• rs2772577
• ENST00000602614.1:n.132+1105G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000602614.1(ENSG00000269957):​n.132+1105G>A variant causes a intron 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: ENSG00000269957 ENST00000602614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 3 publications found

Genes affected

ENSG00000269957 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602614.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000269957	ENST00000602614.1	TSL:3	n.132+1105G>A		intron	N/A
	ENSG00000269957	ENST00000602851.6	TSL:5	n.178+1105G>A		intron	N/A
	ENSG00000269957	ENST00000649380.1		n.192+1105G>A		intron	N/A

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

African (AFR) AF: 0.110 AC: 4561 AN: 41506

American (AMR) AF: 0.171 AC: 2615 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 463 AN: 3466

East Asian (EAS) AF: 0.0497 AC: 257 AN: 5166

South Asian (SAS) AF: 0.114 AC: 548 AN: 4822

European-Finnish (FIN) AF: 0.266 AC: 2806 AN: 10556

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15751 AN: 67978

Other (OTH) AF: 0.182 AC: 384 AN: 2110

Alfa AF: 0.203 Hom.: 5912

Bravo AF: 0.170

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.63
PhyloP100		0.090

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2772577;

hg19: chr9-24547232;