chr11-131305430-G-C

Variant names:

• chr11-131305430-G-C
• rs1114296
• ENST00000606885.1:n.147-44879G>C

Variant summary

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

The ENST00000606885.1(ENSG00000231698):​n.147-44879G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,044 control chromosomes in the GnomAD database, including 5,978 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 0.27 (5978 hom., cov: 32)
• Consequence: ENSG00000231698 ENST00000606885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 4 publications found

Genes affected

ENSG00000231698 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606885.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231698	ENST00000606885.1	TSL:1	n.147-44879G>C		intron	N/A
	ENSG00000231698	ENST00000834706.1		n.185-44879G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40332 AN: 151926 Hom.: 5954 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.266 AC: 40401 AN: 152044 Hom.: 5978 Cov.: 32 AF XY: 0.264 AC XY: 19608 AN XY: 74316

African (AFR) AF: 0.389 AC: 16141 AN: 41450

American (AMR) AF: 0.295 AC: 4496 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3472

East Asian (EAS) AF: 0.325 AC: 1671 AN: 5140

South Asian (SAS) AF: 0.154 AC: 739 AN: 4812

European-Finnish (FIN) AF: 0.163 AC: 1726 AN: 10584

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14014 AN: 67998

Other (OTH) AF: 0.251 AC: 532 AN: 2116

Alfa AF: 0.0981 Hom.: 126

Bravo AF: 0.286

Asia WGS AF: 0.276 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.29
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs1114296; hg19: chr11-131175325;