chr5-150188407-G-A

Variant names:

• chr5-150188407-G-A
• rs3776083

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 0.333 in 152,126 control chromosomes in the GnomAD database, including 9,145 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 0.33 (9145 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 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: 0.334 AC: 50714 AN: 152008 Hom.: 9147 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.333 AC: 50710 AN: 152126 Hom.: 9145 Cov.: 33 AF XY: 0.334 AC XY: 24822 AN XY: 74378

African (AFR) AF: 0.194 AC: 8061 AN: 41516

American (AMR) AF: 0.308 AC: 4700 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1493 AN: 3472

East Asian (EAS) AF: 0.477 AC: 2468 AN: 5174

South Asian (SAS) AF: 0.332 AC: 1599 AN: 4820

European-Finnish (FIN) AF: 0.371 AC: 3924 AN: 10586

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27172 AN: 67958

Other (OTH) AF: 0.372 AC: 786 AN: 2114

Alfa AF: 0.305 Hom.: 5014

Bravo AF: 0.323

Asia WGS AF: 0.372 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.21
DANN	Benign	0.28
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs3776083; hg19: chr5-149567970;