rs11702528

Variant names:

• chr21-17665769-G-A
• rs11702528
• ENST00000416641.2:n.211-5368C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-17665769-G-A
• chr21-17665769-G-C

Variant summary

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

The ENST00000416641.2(ENSG00000226956):​n.211-5368C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,136 control chromosomes in the GnomAD database, including 2,271 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 (2271 hom., cov: 32)
• Consequence: ENSG00000226956 ENST00000416641.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 2 publications found

Genes affected

ENSG00000226956 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416641.2. 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
	ENSG00000226956	ENST00000416641.2	TSL:3	n.211-5368C>T		intron	N/A
	ENSG00000226956	ENST00000813567.1		n.339-6100C>T		intron	N/A
	ENSG00000226956	ENST00000813569.1		n.223-6100C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25019 AN: 152018 Hom.: 2271 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.165 AC: 25031 AN: 152136 Hom.: 2271 Cov.: 32 AF XY: 0.159 AC XY: 11817 AN XY: 74374

African (AFR) AF: 0.124 AC: 5137 AN: 41506

American (AMR) AF: 0.163 AC: 2482 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5186

South Asian (SAS) AF: 0.178 AC: 859 AN: 4828

European-Finnish (FIN) AF: 0.125 AC: 1321 AN: 10564

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.199 AC: 13550 AN: 67996

Other (OTH) AF: 0.198 AC: 419 AN: 2114

Alfa AF: 0.183 Hom.: 662

Bravo AF: 0.165

Asia WGS AF: 0.0820 AC: 287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.79
PhyloP100		-0.27

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: rs11702528;

hg19: chr21-19038087;

COSMIC: COSV53453633;