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. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 4 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.220 AC: 26 AN: 118

Other (OTH) AF: 0.250 AC: 2 AN: 8

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

African (AFR) AF: 0.142 AC: 5899 AN: 41488

American (AMR) AF: 0.158 AC: 2416 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 713 AN: 3466

East Asian (EAS) AF: 0.149 AC: 765 AN: 5150

South Asian (SAS) AF: 0.246 AC: 1179 AN: 4800

European-Finnish (FIN) AF: 0.213 AC: 2256 AN: 10570

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.275 AC: 18699 AN: 67924

Other (OTH) AF: 0.205 AC: 434 AN: 2112

Alfa AF: 0.238 Hom.: 5825

Bravo AF: 0.205

Asia WGS AF: 0.182 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-0.72
PromoterAI		-0.014	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11646957; hg19: chr16-24267309;