rs2018964

Variant names:

• chr4-155386292-A-G
• rs2018964

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 0.0976 in 152,106 control chromosomes in the GnomAD database, including 1,727 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 0.098 (1727 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 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: 0.0974 AC: 14809 AN: 151988 Hom.: 1719 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.00754

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0976 AC: 14850 AN: 152106 Hom.: 1727 Cov.: 32 AF XY: 0.0959 AC XY: 7129 AN XY: 74368

African (AFR) AF: 0.283 AC: 11711 AN: 41446

American (AMR) AF: 0.0454 AC: 693 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3470

East Asian (EAS) AF: 0.122 AC: 633 AN: 5180

South Asian (SAS) AF: 0.0509 AC: 245 AN: 4812

European-Finnish (FIN) AF: 0.00754 AC: 80 AN: 10606

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0158 AC: 1077 AN: 68006

Other (OTH) AF: 0.0829 AC: 175 AN: 2112

Alfa AF: 0.0641 Hom.: 163

Bravo AF: 0.109

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.74
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs2018964; hg19: chr4-156307444;