chr16-59315628-T-C

Variant names:

• chr16-59315628-T-C
• rs925338

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 0.0753 in 152,264 control chromosomes in the GnomAD database, including 927 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 0.075 (927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 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: 0.0753 AC: 11459 AN: 152146 Hom.: 929 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0589

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0236

Gnomad OTH AF: 0.0771

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

GnomAD4 genome AF: 0.0753 AC: 11464 AN: 152264 Hom.: 927 Cov.: 32 AF XY: 0.0803 AC XY: 5975 AN XY: 74454

African (AFR) AF: 0.119 AC: 4925 AN: 41544

American (AMR) AF: 0.0590 AC: 903 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0757 AC: 263 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2059 AN: 5164

South Asian (SAS) AF: 0.226 AC: 1092 AN: 4822

European-Finnish (FIN) AF: 0.0399 AC: 423 AN: 10614

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0237 AC: 1610 AN: 68028

Other (OTH) AF: 0.0777 AC: 164 AN: 2110

Alfa AF: 0.0451 Hom.: 1570

Bravo AF: 0.0782

Asia WGS AF: 0.252 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.60
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs925338; hg19: chr16-59349532;