11-128319206-A-G

Variant names:

• chr11-128319206-A-G
• rs4937314
• ENST00000826985.1:n.210-4980T>C

Variant summary

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

The ENST00000826985.1(ENSG00000307544):​n.210-4980T>C 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 151,828 control chromosomes in the GnomAD database, including 2,006 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 (2006 hom., cov: 31)
• Consequence: ENSG00000307544 ENST00000826985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 7 publications found

Genes affected

ENSG00000307544 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826985.1. 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
	ENSG00000307544	ENST00000826985.1		n.210-4980T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24363 AN: 151740 Hom.: 2002 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.161 AC: 24374 AN: 151828 Hom.: 2006 Cov.: 31 AF XY: 0.160 AC XY: 11879 AN XY: 74196

African (AFR) AF: 0.146 AC: 6036 AN: 41362

American (AMR) AF: 0.161 AC: 2463 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 888 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1082 AN: 5152

South Asian (SAS) AF: 0.192 AC: 920 AN: 4800

European-Finnish (FIN) AF: 0.131 AC: 1377 AN: 10526

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.163 AC: 11064 AN: 67950

Other (OTH) AF: 0.187 AC: 392 AN: 2100

Alfa AF: 0.168 Hom.: 6406

Bravo AF: 0.162

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.69
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs4937314; hg19: chr11-128189101;