11-81275763-T-C

Position:

• chr11-81275763-T-C

Variant summary

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

The ENST00000701193.1(ENSG00000287912):​n.218+783T>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 0.162 in 152,082 control chromosomes in the GnomAD database, including 2,238 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 0.16 (2238 hom., cov: 32)
• Consequence: ENST00000701193.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701193.1	n.218+783T>C		intron_variant, non_coding_transcript_variant
	ENST00000671134.1	n.428+783T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24678 AN: 151966 Hom.: 2238 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.162 AC: 24686 AN: 152082 Hom.: 2238 Cov.: 32 AF XY: 0.159 AC XY: 11831 AN XY: 74354

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0975

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.175

Alfa AF: 0.153 Hom.: 2593

Bravo AF: 0.171

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501500; hg19: chr11-80986806;