rs7186407

Variant names:

• chr16-54803156-A-T
• rs7186407

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 0.432 in 151,974 control chromosomes in the GnomAD database, including 15,490 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 0.43 (15490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 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: 0.432 AC: 65653 AN: 151856 Hom.: 15489 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.0358

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.432 AC: 65664 AN: 151974 Hom.: 15490 Cov.: 32 AF XY: 0.428 AC XY: 31782 AN XY: 74274

African (AFR) AF: 0.327 AC: 13565 AN: 41420

American (AMR) AF: 0.407 AC: 6218 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3466

East Asian (EAS) AF: 0.0360 AC: 186 AN: 5162

South Asian (SAS) AF: 0.250 AC: 1207 AN: 4824

European-Finnish (FIN) AF: 0.571 AC: 6030 AN: 10566

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35437 AN: 67956

Other (OTH) AF: 0.427 AC: 900 AN: 2110

Alfa AF: 0.480 Hom.: 2208

Bravo AF: 0.418

Asia WGS AF: 0.145 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.47
DANN	Benign	0.74
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs7186407; hg19: chr16-54837068;