11-15708965-T-G

Variant names:

• chr11-15708965-T-G
• rs11827785
• ENST00000524613.1:n.448-1871A>C

Variant summary

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

The ENST00000524613.1(ENSG00000254645):​n.448-1871A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,022 control chromosomes in the GnomAD database, including 6,042 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 0.27 (6042 hom., cov: 32)
• Consequence: ENSG00000254645 ENST00000524613.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219
• Publications: 5 publications found

Genes affected

ENSG00000254645 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376567	XR_001748140.2	n.573-4345A>C		intron_variant	Intron 4 of 6
LOC105376567	XR_001748141.2	n.260-4345A>C		intron_variant	Intron 1 of 4
LOC105376567	XR_002957238.2	n.461-4345A>C		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254645	ENST00000524613.1	n.448-1871A>C		intron_variant	Intron 4 of 8	5
ENSG00000254645	ENST00000663676.1	n.498-1871A>C		intron_variant	Intron 4 of 7
ENSG00000254645	ENST00000727850.1	n.287-4345A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40495 AN: 151904 Hom.: 6031 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.267 AC: 40532 AN: 152022 Hom.: 6042 Cov.: 32 AF XY: 0.269 AC XY: 20001 AN XY: 74300

African (AFR) AF: 0.386 AC: 15994 AN: 41430

American (AMR) AF: 0.229 AC: 3497 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3466

East Asian (EAS) AF: 0.214 AC: 1105 AN: 5174

South Asian (SAS) AF: 0.120 AC: 577 AN: 4810

European-Finnish (FIN) AF: 0.355 AC: 3746 AN: 10556

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13792 AN: 67982

Other (OTH) AF: 0.255 AC: 537 AN: 2106

Alfa AF: 0.163 Hom.: 447

Bravo AF: 0.270

Asia WGS AF: 0.208 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.54
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs11827785; hg19: chr11-15730511;