rs11265260

Variant names:

• chr1-159730249-A-G
• rs11265260
• ENST00000751816.1:n.244+3586A>G

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.244+3586A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 152,228 control chromosomes in the GnomAD database, including 446 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 0.069 (446 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.748
• Publications: 31 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. 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
	ENSG00000297913	ENST00000751816.1		n.244+3586A>G		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.356+3075A>G		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.199+3586A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 10551 AN: 152110 Hom.: 444 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.0693 AC: 10557 AN: 152228 Hom.: 446 Cov.: 32 AF XY: 0.0699 AC XY: 5206 AN XY: 74436

African (AFR) AF: 0.0704 AC: 2922 AN: 41534

American (AMR) AF: 0.0565 AC: 864 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3470

East Asian (EAS) AF: 0.152 AC: 785 AN: 5176

South Asian (SAS) AF: 0.108 AC: 522 AN: 4822

European-Finnish (FIN) AF: 0.0651 AC: 690 AN: 10606

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0607 AC: 4128 AN: 68004

Other (OTH) AF: 0.0866 AC: 183 AN: 2112

Alfa AF: 0.0659 Hom.: 1209

Bravo AF: 0.0684

Asia WGS AF: 0.0900 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.63
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs11265260; hg19: chr1-159700039;