rs11235965

Variant names:

• chr11-73995246-C-T
• rs11235965
• ENST00000544832.1:n.906G>A

Variant summary

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

The ENST00000544832.1(ENSG00000256723):​n.906G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 156,904 control chromosomes in the GnomAD database, including 4,236 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 0.22 (4029 hom., cov: 32)
  • Exomes 𝑓: 0.29 (207 hom.)
• Consequence: ENSG00000256723 ENST00000544832.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 5 publications found

Genes affected

ENSG00000256723 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000544832.1. 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
	ENSG00000256723	ENST00000544832.1	TSL:6	n.906G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33514 AN: 151948 Hom.: 4032 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.289 AC: 1399 AN: 4836 Hom.: 207 Cov.: 0 AF XY: 0.280 AC XY: 891 AN XY: 3180

African (AFR) AF: 0.155 AC: 9 AN: 58

American (AMR) AF: 0.261 AC: 12 AN: 46

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 10 AN: 52

East Asian (EAS) AF: 0.303 AC: 54 AN: 178

South Asian (SAS) AF: 0.213 AC: 122 AN: 574

European-Finnish (FIN) AF: 0.387 AC: 385 AN: 994

Middle Eastern (MID) AF: 0.143 AC: 4 AN: 28

European-Non Finnish (NFE) AF: 0.278 AC: 752 AN: 2704

Other (OTH) AF: 0.252 AC: 51 AN: 202

GnomAD4 genome AF: 0.220 AC: 33516 AN: 152068 Hom.: 4029 Cov.: 32 AF XY: 0.225 AC XY: 16752 AN XY: 74318

African (AFR) AF: 0.166 AC: 6893 AN: 41476

American (AMR) AF: 0.147 AC: 2243 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3472

East Asian (EAS) AF: 0.293 AC: 1519 AN: 5178

South Asian (SAS) AF: 0.241 AC: 1158 AN: 4810

European-Finnish (FIN) AF: 0.381 AC: 4019 AN: 10554

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16393 AN: 67980

Other (OTH) AF: 0.184 AC: 389 AN: 2112

Alfa AF: 0.227 Hom.: 676

Bravo AF: 0.197

Asia WGS AF: 0.246 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	6.0
DANN	Benign	0.64
PhyloP100		-0.017

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: rs11235965;

hg19: chr11-73706291;