rs1272496

Variant names:

• chr11-130504156-G-A
• rs1272496
• ENST00000777947.1:n.221+26146G>A

Variant summary

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

The ENST00000777947.1(ENSG00000301321):​n.221+26146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,092 control chromosomes in the GnomAD database, including 3,614 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 0.21 (3614 hom., cov: 32)
• Consequence: ENSG00000301321 ENST00000777947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 2 publications found

Genes affected

ENSG00000301321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301321	ENST00000777947.1	n.221+26146G>A		intron_variant	Intron 2 of 3
ENSG00000301321	ENST00000777948.1	n.431+26146G>A		intron_variant	Intron 2 of 3
ENSG00000301321	ENST00000777949.1	n.560+25422G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31614 AN: 151974 Hom.: 3614 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.00867

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.208 AC: 31626 AN: 152092 Hom.: 3614 Cov.: 32 AF XY: 0.204 AC XY: 15166 AN XY: 74352

African (AFR) AF: 0.164 AC: 6806 AN: 41484

American (AMR) AF: 0.196 AC: 2994 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 914 AN: 3466

East Asian (EAS) AF: 0.00869 AC: 45 AN: 5178

South Asian (SAS) AF: 0.146 AC: 702 AN: 4814

European-Finnish (FIN) AF: 0.189 AC: 2005 AN: 10584

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17396 AN: 67982

Other (OTH) AF: 0.240 AC: 507 AN: 2110

Alfa AF: 0.220 Hom.: 503

Bravo AF: 0.209

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	11
DANN	Benign	0.89
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1272496; hg19: chr11-130374051;