11-86703240-A-G

Variant names:

• chr11-86703240-A-G
• rs2512987
• ENST00000716175.1:n.235+30789A>G

Variant summary

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

The ENST00000716175.1(ENSG00000255250):​n.235+30789A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,022 control chromosomes in the GnomAD database, including 16,795 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 0.47 (16785 hom., cov: 32)
  • Exomes 𝑓: 0.55 (10 hom.)
• Consequence: ENSG00000255250 ENST00000716175.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 4 publications found

Genes affected

ENSG00000255250 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 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
ENSG00000255250	ENST00000716175.1	n.235+30789A>G		intron_variant	Intron 1 of 4
ENSG00000255250	ENST00000716176.1	n.387+113A>G		intron_variant	Intron 3 of 6
ENSG00000255250	ENST00000716177.1	n.340+113A>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70864 AN: 151842 Hom.: 16776 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.429

GnomAD4 exome AF: 0.545 AC: 36 AN: 66 Hom.: 10 AF XY: 0.533 AC XY: 16 AN XY: 30

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.536 AC: 30 AN: 56

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.625 AC: 5 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.467 AC: 70915 AN: 151956 Hom.: 16785 Cov.: 32 AF XY: 0.467 AC XY: 34704 AN XY: 74280

African (AFR) AF: 0.484 AC: 20066 AN: 41418

American (AMR) AF: 0.391 AC: 5977 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1386 AN: 3466

East Asian (EAS) AF: 0.307 AC: 1582 AN: 5156

South Asian (SAS) AF: 0.452 AC: 2178 AN: 4814

European-Finnish (FIN) AF: 0.581 AC: 6137 AN: 10566

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32300 AN: 67932

Other (OTH) AF: 0.427 AC: 903 AN: 2116

Alfa AF: 0.462 Hom.: 65989

Bravo AF: 0.450

Asia WGS AF: 0.397 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2512987; hg19: chr11-86414282;