rs11700697

Positions:

• chr21-44995960-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.33 in 152,084 control chromosomes in the GnomAD database, including 9,889 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 0.33 (9889 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50211 AN: 151966 Hom.: 9893 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.330 AC: 50215 AN: 152084 Hom.: 9889 Cov.: 33 AF XY: 0.335 AC XY: 24940 AN XY: 74338

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.347

Alfa AF: 0.384 Hom.: 2410

Bravo AF: 0.309

Asia WGS AF: 0.432 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11700697; hg19: chr21-46415875;