chr11-17479663-G-A

Variant names:

• chr11-17479663-G-A
• rs3758947
• ENST00000662030.2:n.200+2932G>A

Variant summary

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

The ENST00000662030.2(ENSG00000287898):​n.200+2932G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,052 control chromosomes in the GnomAD database, including 2,544 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 (2544 hom., cov: 32)
• Consequence: ENSG00000287898 ENST00000662030.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.898
• Publications: 14 publications found

Genes affected

ENSG00000287898 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902641	XR_007062609.1	n.81+2932G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287898	ENST00000662030.2	n.200+2932G>A		intron_variant	Intron 1 of 1
ENSG00000287898	ENST00000666786.2	n.153+2609G>A		intron_variant	Intron 1 of 1
ENSG00000287898	ENST00000719322.1	n.150+3377G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24438 AN: 151934 Hom.: 2546 Cov.: 32

Gnomad AFR AF: 0.0405

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.161 AC: 24434 AN: 152052 Hom.: 2544 Cov.: 32 AF XY: 0.167 AC XY: 12426 AN XY: 74300

African (AFR) AF: 0.0404 AC: 1678 AN: 41508

American (AMR) AF: 0.272 AC: 4151 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3472

East Asian (EAS) AF: 0.266 AC: 1373 AN: 5158

South Asian (SAS) AF: 0.233 AC: 1123 AN: 4810

European-Finnish (FIN) AF: 0.245 AC: 2587 AN: 10548

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12569 AN: 67968

Other (OTH) AF: 0.132 AC: 278 AN: 2112

Alfa AF: 0.175 Hom.: 4362

Bravo AF: 0.159

Asia WGS AF: 0.237 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.1
DANN	Benign	0.80
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs3758947; hg19: chr11-17501210;