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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904999	XR_007067821.1	n.65-6100C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226956	ENST00000416641.2	n.211-5368C>T		intron_variant	Intron 1 of 2	3
ENSG00000226956	ENST00000813567.1	n.339-6100C>T		intron_variant	Intron 1 of 1
ENSG00000226956	ENST00000813569.1	n.223-6100C>T		intron_variant	Intron 1 of 1
ENSG00000226956	ENST00000813570.1	n.100+4998C>T		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs11702528; hg19: chr21-19038087; COSMIC: COSV53453633;