rs11571297

Variant names:

• chr2-203880280-T-C
• rs11571297

Variant summary

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

The variant allele was found at a frequency of 0.442 in 151,920 control chromosomes in the GnomAD database, including 15,110 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 0.44 (15110 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67053 AN: 151800 Hom.: 15113 Cov.: 31

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.442 AC: 67073 AN: 151920 Hom.: 15110 Cov.: 31 AF XY: 0.437 AC XY: 32472 AN XY: 74228

African (AFR) AF: 0.388 AC: 16058 AN: 41406

American (AMR) AF: 0.461 AC: 7042 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1823 AN: 3464

East Asian (EAS) AF: 0.295 AC: 1524 AN: 5168

South Asian (SAS) AF: 0.623 AC: 3000 AN: 4818

European-Finnish (FIN) AF: 0.358 AC: 3770 AN: 10544

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32276 AN: 67936

Other (OTH) AF: 0.489 AC: 1030 AN: 2106

Alfa AF: 0.471 Hom.: 5000

Bravo AF: 0.441

Asia WGS AF: 0.497 AC: 1728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs11571297; hg19: chr2-204745003;