rs7193788

Variant names:

• chr16-82622555-A-G
• rs7193788

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 0.165 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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.142 AC: 5886 AN: 41580

American (AMR) AF: 0.147 AC: 2246 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0821 AC: 285 AN: 3472

East Asian (EAS) AF: 0.489 AC: 2529 AN: 5170

South Asian (SAS) AF: 0.224 AC: 1082 AN: 4822

European-Finnish (FIN) AF: 0.236 AC: 2501 AN: 10612

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10149 AN: 68028

Other (OTH) AF: 0.153 AC: 323 AN: 2112

Alfa AF: 0.159 Hom.: 1633

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs7193788; hg19: chr16-82656160;