rs11021203

Variant names:

• chr11-95544896-G-C
• rs11021203
• ENST00000816277.1:n.603-27762C>G

Your query was ambiguous. Multiple possible variants found:

• chr11-95544896-G-C
• chr11-95544896-G-T

Variant summary

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

The ENST00000816277.1(ENSG00000306211):​n.603-27762C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,186 control chromosomes in the GnomAD database, including 1,309 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 0.12 (1309 hom., cov: 32)
• Consequence: ENSG00000306211 ENST00000816277.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.916
• Publications: 2 publications found

Genes affected

ENSG00000306211 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816277.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306211	ENST00000816277.1		n.603-27762C>G		intron	N/A
	ENSG00000306211	ENST00000816280.1		n.205-27762C>G		intron	N/A
	ENSG00000306211	ENST00000816281.1		n.202-26822C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18251 AN: 152068 Hom.: 1308 Cov.: 32

Gnomad AFR AF: 0.0494

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.120 AC: 18262 AN: 152186 Hom.: 1309 Cov.: 32 AF XY: 0.119 AC XY: 8842 AN XY: 74398

African (AFR) AF: 0.0493 AC: 2049 AN: 41532

American (AMR) AF: 0.109 AC: 1671 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3472

East Asian (EAS) AF: 0.144 AC: 743 AN: 5172

South Asian (SAS) AF: 0.155 AC: 748 AN: 4812

European-Finnish (FIN) AF: 0.127 AC: 1346 AN: 10602

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10946 AN: 67986

Other (OTH) AF: 0.129 AC: 272 AN: 2112

Alfa AF: 0.135 Hom.: 195

Bravo AF: 0.114

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	13
DANN	Benign	0.74
PhyloP100		0.92

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11021203;

hg19: chr11-95278060;