chr4-99354745-G-A

Variant names:

• chr4-99354745-G-A
• rs1693469

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 0.314 in 152,038 control chromosomes in the GnomAD database, including 8,904 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 0.31 (8904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.955
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 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: 0.314 AC: 47670 AN: 151918 Hom.: 8897 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.0821

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.314 AC: 47694 AN: 152038 Hom.: 8904 Cov.: 32 AF XY: 0.314 AC XY: 23365 AN XY: 74314

African (AFR) AF: 0.144 AC: 5977 AN: 41514

American (AMR) AF: 0.294 AC: 4487 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3468

East Asian (EAS) AF: 0.0817 AC: 421 AN: 5150

South Asian (SAS) AF: 0.307 AC: 1478 AN: 4810

European-Finnish (FIN) AF: 0.514 AC: 5425 AN: 10552

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28032 AN: 67954

Other (OTH) AF: 0.289 AC: 608 AN: 2106

Alfa AF: 0.365 Hom.: 1482

Bravo AF: 0.288

Asia WGS AF: 0.222 AC: 770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.14
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs1693469; hg19: chr4-100275902;