chr16-55713034-A-C

Variant names:

• chr16-55713034-A-C
• rs1948773

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 0.0926 in 152,150 control chromosomes in the GnomAD database, including 716 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 0.093 (716 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 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: 0.0927 AC: 14095 AN: 152032 Hom.: 715 Cov.: 31

Gnomad AFR AF: 0.0462

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0926

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0926 AC: 14086 AN: 152150 Hom.: 716 Cov.: 31 AF XY: 0.0948 AC XY: 7047 AN XY: 74374

African (AFR) AF: 0.0459 AC: 1907 AN: 41528

American (AMR) AF: 0.0924 AC: 1411 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3470

East Asian (EAS) AF: 0.196 AC: 1010 AN: 5148

South Asian (SAS) AF: 0.134 AC: 646 AN: 4820

European-Finnish (FIN) AF: 0.115 AC: 1216 AN: 10592

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7097 AN: 68004

Other (OTH) AF: 0.105 AC: 222 AN: 2108

Alfa AF: 0.102 Hom.: 1069

Bravo AF: 0.0901

Asia WGS AF: 0.156 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.45
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1948773; hg19: chr16-55746946;