rs11683503

Variant names:

• chr2-78971042-T-C
• rs11683503

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 0.167 in 152,082 control chromosomes in the GnomAD database, including 3,240 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 0.17 (3240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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: 0.167 AC: 25369 AN: 151964 Hom.: 3231 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0849

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0835

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.167 AC: 25429 AN: 152082 Hom.: 3240 Cov.: 32 AF XY: 0.167 AC XY: 12386 AN XY: 74376

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.0700

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0849

Gnomad4 NFE AF: 0.0835

Gnomad4 OTH AF: 0.147

Alfa AF: 0.0979 Hom.: 1298

Bravo AF: 0.176

Asia WGS AF: 0.173 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11683503; hg19: chr2-79198168;