rs116875324

Variant names:

• chr11-121335740-C-T
• rs116875324
• ENST00000761170.1:n.329-22569G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000761170.1(ENSG00000299150):​n.329-22569G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.017 in 152,270 control chromosomes in the GnomAD database, including 53 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 0.017 (53 hom., cov: 33)
• Consequence: ENSG00000299150 ENST00000761170.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 2 publications found

Genes affected

ENSG00000299150 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.017 (2588/152270) while in subpopulation NFE AF = 0.0185 (1261/68030). AF 95% confidence interval is 0.0177. There are 53 homozygotes in GnomAd4. There are 1447 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 53 gene

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
ENSG00000299150	ENST00000761170.1	n.329-22569G>A		intron_variant	Intron 1 of 2
ENSG00000299150	ENST00000761171.1	n.319-1216G>A		intron_variant	Intron 2 of 4
ENSG00000299150	ENST00000761172.1	n.198-1216G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0170 AC: 2588 AN: 152152 Hom.: 53 Cov.: 33

Gnomad AFR AF: 0.00241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0137

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.0902

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.00861

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

GnomAD4 genome AF: 0.0170 AC: 2588 AN: 152270 Hom.: 53 Cov.: 33 AF XY: 0.0194 AC XY: 1447 AN XY: 74436

African (AFR) AF: 0.00241 AC: 100 AN: 41548

American (AMR) AF: 0.0137 AC: 209 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00922 AC: 32 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.00228 AC: 11 AN: 4822

European-Finnish (FIN) AF: 0.0902 AC: 955 AN: 10590

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0185 AC: 1261 AN: 68030

Other (OTH) AF: 0.00852 AC: 18 AN: 2112

Alfa AF: 0.0170 Hom.: 37

Bravo AF: 0.0109

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.86
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs116875324; hg19: chr11-121206449;