4-99322140-G-A

Variant names:

• chr4-99322140-G-A
• rs2070898

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 0.233 in 152,132 control chromosomes in the GnomAD database, including 5,586 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 0.23 (5586 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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: 0.234 AC: 35509 AN: 152014 Hom.: 5595 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.233 AC: 35490 AN: 152132 Hom.: 5586 Cov.: 32 AF XY: 0.237 AC XY: 17632 AN XY: 74374

African (AFR) AF: 0.0958 AC: 3978 AN: 41522

American (AMR) AF: 0.186 AC: 2848 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 823 AN: 3468

East Asian (EAS) AF: 0.800 AC: 4132 AN: 5166

South Asian (SAS) AF: 0.480 AC: 2308 AN: 4812

European-Finnish (FIN) AF: 0.201 AC: 2124 AN: 10592

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18394 AN: 67980

Other (OTH) AF: 0.239 AC: 504 AN: 2112

Alfa AF: 0.250 Hom.: 648

Bravo AF: 0.223

Asia WGS AF: 0.474 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.65
DANN	Benign	0.68
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2070898; hg19: chr4-100243297;