rs444984

Variant names:

• chr5-155067396-C-A
• rs444984

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 0.42 in 152,010 control chromosomes in the GnomAD database, including 15,063 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 0.42 (15063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.534 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: 0.420 AC: 63778 AN: 151890 Hom.: 15062 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.420 AC: 63786 AN: 152010 Hom.: 15063 Cov.: 32 AF XY: 0.422 AC XY: 31326 AN XY: 74282

African (AFR) AF: 0.205 AC: 8494 AN: 41458

American (AMR) AF: 0.432 AC: 6607 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1660 AN: 3468

East Asian (EAS) AF: 0.214 AC: 1104 AN: 5166

South Asian (SAS) AF: 0.520 AC: 2501 AN: 4814

European-Finnish (FIN) AF: 0.496 AC: 5239 AN: 10554

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.538 AC: 36576 AN: 67952

Other (OTH) AF: 0.433 AC: 912 AN: 2108

Alfa AF: 0.491 Hom.: 52536

Bravo AF: 0.399

Asia WGS AF: 0.357 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	14
DANN	Benign	0.92
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs444984; hg19: chr5-154446956;