rs11646957

Variant names:

• chr16-24255988-C-A
• rs11646957

Your query was ambiguous. Multiple possible variants found:

• chr16-24255988-C-A
• chr16-24255988-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 0.214 in 152,152 control chromosomes in the GnomAD database, including 3,853 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 0.21 (3850 hom., cov: 32)
  • Exomes 𝑓: 0.23 (3 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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: 0.214 AC: 32543 AN: 151894 Hom.: 3846 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.205

GnomAD4 exome AF: 0.225 AC: 32 AN: 142 Hom.: 3 Cov.: 0 AF XY: 0.240 AC XY: 25 AN XY: 104

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.220

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.214 AC: 32560 AN: 152010 Hom.: 3850 Cov.: 32 AF XY: 0.212 AC XY: 15751 AN XY: 74292

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.205

Alfa AF: 0.242 Hom.: 4538

Bravo AF: 0.205

Asia WGS AF: 0.182 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11646957; hg19: chr16-24267309;