11-15708965-T-G

Position:

• chr11-15708965-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663676.1(ENSG00000254645):​n.498-1871A>C variant causes a intron, non coding transcript 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: ENST00000663676.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105376567	XR_001748141.2	n.260-4345A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663676.1	n.498-1871A>C		intron_variant, non_coding_transcript_variant
	ENST00000524613.1	n.448-1871A>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.255

Alfa AF: 0.154 Hom.: 390

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11827785; hg19: chr11-15730511;