4-60905713-A-G

Variant names:

• chr4-60905713-A-G
• rs1455280
• ENST00000756310.1:n.243-9256A>G

Variant summary

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

The ENST00000756310.1(ENSG00000298540):​n.243-9256A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,108 control chromosomes in the GnomAD database, including 1,046 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 0.11 (1046 hom., cov: 32)
• Consequence: ENSG00000298540 ENST00000756310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.773
• Publications: 6 publications found

Genes affected

ENSG00000298540 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756310.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298540	ENST00000756310.1		n.243-9256A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16777 AN: 151990 Hom.: 1043 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.110 AC: 16798 AN: 152108 Hom.: 1046 Cov.: 32 AF XY: 0.108 AC XY: 8028 AN XY: 74360

African (AFR) AF: 0.119 AC: 4919 AN: 41506

American (AMR) AF: 0.0889 AC: 1356 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 844 AN: 3466

East Asian (EAS) AF: 0.0159 AC: 82 AN: 5170

South Asian (SAS) AF: 0.143 AC: 691 AN: 4830

European-Finnish (FIN) AF: 0.0640 AC: 679 AN: 10604

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7814 AN: 67960

Other (OTH) AF: 0.127 AC: 268 AN: 2116

Alfa AF: 0.121 Hom.: 1923

Bravo AF: 0.112

Asia WGS AF: 0.0920 AC: 321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.6
DANN	Benign	0.67
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs1455280; hg19: chr4-61771431;