11-111017760-C-T

Variant names:

• chr11-111017760-C-T
• rs978769
• ENST00000660486.1:n.50+4259C>T

Variant summary

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

The ENST00000660486.1(ENSG00000287556):​n.50+4259C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,998 control chromosomes in the GnomAD database, including 11,475 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 0.38 (11475 hom., cov: 32)
• Consequence: ENSG00000287556 ENST00000660486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 4 publications found

Genes affected

ENSG00000287556 (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 (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369489	XR_948009.2	n.1464+712G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287556	ENST00000660486.1	n.50+4259C>T		intron_variant	Intron 1 of 1
ENSG00000299094	ENST00000760419.1	n.384+712G>A		intron_variant	Intron 2 of 2
ENSG00000299094	ENST00000760420.1	n.582+712G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57108 AN: 151880 Hom.: 11459 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.376 AC: 57165 AN: 151998 Hom.: 11475 Cov.: 32 AF XY: 0.386 AC XY: 28671 AN XY: 74270

African (AFR) AF: 0.391 AC: 16201 AN: 41428

American (AMR) AF: 0.394 AC: 6019 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1443 AN: 3468

East Asian (EAS) AF: 0.787 AC: 4077 AN: 5182

South Asian (SAS) AF: 0.658 AC: 3160 AN: 4804

European-Finnish (FIN) AF: 0.326 AC: 3445 AN: 10564

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.318 AC: 21622 AN: 67960

Other (OTH) AF: 0.386 AC: 816 AN: 2112

Alfa AF: 0.345 Hom.: 29619

Bravo AF: 0.379

Asia WGS AF: 0.690 AC: 2397 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	2.2
DANN	Benign	0.76
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs978769; hg19: chr11-110888484;