rs7193788

Variant names:

• chr16-82622555-A-G
• rs7193788

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.165 in 152,306 control chromosomes in the GnomAD database, including 2,465 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 0.17 (2465 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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: 0.165 AC: 25167 AN: 152188 Hom.: 2467 Cov.: 34

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.165 AC: 25163 AN: 152306 Hom.: 2465 Cov.: 34 AF XY: 0.171 AC XY: 12703 AN XY: 74478

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0821

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.153

Alfa AF: 0.152 Hom.: 967

Bravo AF: 0.159

Asia WGS AF: 0.320 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7193788; hg19: chr16-82656160;