16-31557521-C-T

Variant names:

• chr16-31557521-C-T
• rs6565249

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 0.128 in 152,234 control chromosomes in the GnomAD database, including 2,106 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 0.13 (2106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 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: 0.128 AC: 19492 AN: 152116 Hom.: 2103 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.0810

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.0393

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0533

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.128 AC: 19505 AN: 152234 Hom.: 2106 Cov.: 32 AF XY: 0.132 AC XY: 9823 AN XY: 74442

African (AFR) AF: 0.257 AC: 10666 AN: 41514

American (AMR) AF: 0.0709 AC: 1085 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0810 AC: 281 AN: 3470

East Asian (EAS) AF: 0.211 AC: 1089 AN: 5168

South Asian (SAS) AF: 0.386 AC: 1861 AN: 4818

European-Finnish (FIN) AF: 0.0393 AC: 417 AN: 10616

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0534 AC: 3630 AN: 68034

Other (OTH) AF: 0.119 AC: 252 AN: 2114

Alfa AF: 0.0865 Hom.: 435

Bravo AF: 0.128

Asia WGS AF: 0.341 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.79
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6565249; hg19: chr16-31568842;