rs955423

Variant names:

• chr5-166292645-C-A
• rs955423

Your query was ambiguous. Multiple possible variants found:

• chr5-166292645-C-A
• chr5-166292645-C-G

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 0.556 in 151,900 control chromosomes in the GnomAD database, including 23,804 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 0.56 (23804 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.595 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: 0.556 AC: 84388 AN: 151782 Hom.: 23799 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.556 AC: 84430 AN: 151900 Hom.: 23804 Cov.: 31 AF XY: 0.555 AC XY: 41222 AN XY: 74218

African (AFR) AF: 0.498 AC: 20619 AN: 41374

American (AMR) AF: 0.465 AC: 7098 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2141 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2680 AN: 5144

South Asian (SAS) AF: 0.603 AC: 2906 AN: 4818

European-Finnish (FIN) AF: 0.614 AC: 6489 AN: 10570

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40769 AN: 67940

Other (OTH) AF: 0.528 AC: 1115 AN: 2110

Alfa AF: 0.573 Hom.: 68932

Bravo AF: 0.538

Asia WGS AF: 0.523 AC: 1821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.51
DANN	Benign	0.25
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs955423; hg19: chr5-165719650;