rs11917060

Variant names:

• chr3-186536644-G-C
• rs11917060
• ENST00000727128.1:n.187+14824G>C

Variant summary

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

The ENST00000727128.1(ENSG00000294974):​n.187+14824G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,122 control chromosomes in the GnomAD database, including 3,976 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 0.21 (3976 hom., cov: 32)
• Consequence: ENSG00000294974 ENST00000727128.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 2 publications found

Genes affected

ENSG00000294974 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294974	ENST00000727128.1	n.187+14824G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31955 AN: 152004 Hom.: 3968 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.210 AC: 31983 AN: 152122 Hom.: 3976 Cov.: 32 AF XY: 0.213 AC XY: 15869 AN XY: 74372

African (AFR) AF: 0.339 AC: 14075 AN: 41470

American (AMR) AF: 0.204 AC: 3119 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 661 AN: 3472

East Asian (EAS) AF: 0.131 AC: 681 AN: 5184

South Asian (SAS) AF: 0.230 AC: 1107 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2144 AN: 10566

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9619 AN: 67996

Other (OTH) AF: 0.217 AC: 458 AN: 2106

Alfa AF: 0.185 Hom.: 441

Bravo AF: 0.215

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.4
DANN	Benign	0.80
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs11917060; hg19: chr3-186254433;