rs11574514

chr16-67937477-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0292 in 152,336 control chromosomes in the GnomAD database, including 93 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 0.029 (93 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0292 (4445/152336) while in subpopulation NFE AF= 0.0417 (2834/68030). AF 95% confidence interval is 0.0404. There are 93 homozygotes in gnomad4. There are 2054 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 93 gene

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: 0.0292 AC: 4448 AN: 152218 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.00931

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0351

Gnomad ASJ AF: 0.0541

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.00806

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0416

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0292 AC: 4445 AN: 152336 Hom.: 93 Cov.: 32 AF XY: 0.0276 AC XY: 2054 AN XY: 74494

Gnomad4 AFR AF: 0.00931

Gnomad4 AMR AF: 0.0351

Gnomad4 ASJ AF: 0.0541

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.00807

Gnomad4 FIN AF: 0.0251

Gnomad4 NFE AF: 0.0417

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0411 Hom.: 149

Bravo AF: 0.0285

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
Cadd	Benign	5.9
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11574514; hg19: chr16-67971380; COSMIC: COSV50453487;