rs76720124

chr16-57356626-G-C

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 0.00651 in 152,316 control chromosomes in the GnomAD database, including 27 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 0.0065 (27 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00651 (992/152316) while in subpopulation EAS AF= 0.0488 (253/5180). AF 95% confidence interval is 0.0439. There are 27 homozygotes in gnomad4. There are 569 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 26 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: 0.00648 AC: 986 AN: 152198 Hom.: 26 Cov.: 32

Gnomad AFR AF: 0.00106

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0306

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0489

Gnomad SAS AF: 0.00248

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000720

Gnomad OTH AF: 0.00622

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

GnomAD4 genome AF: 0.00651 AC: 992 AN: 152316 Hom.: 27 Cov.: 32 AF XY: 0.00764 AC XY: 569 AN XY: 74486

Gnomad4 AFR AF: 0.00106

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0488

Gnomad4 SAS AF: 0.00269

Gnomad4 FIN AF: 0.0138

Gnomad4 NFE AF: 0.000720

Gnomad4 OTH AF: 0.00616

Alfa AF: 0.00524 Hom.: 4

Bravo AF: 0.00914

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.7
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs76720124; hg19: chr16-57390538;