rs1555543

Variant names:

• chr1-96479241-A-C
• rs1555543

Your query was ambiguous. Multiple possible variants found:

• chr1-96479241-A-C
• chr1-96479241-A-G
• chr1-96479241-A-T

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 0.55 in 151,910 control chromosomes in the GnomAD database, including 23,633 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 0.55 (23633 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 118 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83506 AN: 151794 Hom.: 23632 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.550 AC: 83534 AN: 151910 Hom.: 23633 Cov.: 31 AF XY: 0.550 AC XY: 40790 AN XY: 74214

African (AFR) AF: 0.430 AC: 17817 AN: 41398

American (AMR) AF: 0.581 AC: 8875 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1881 AN: 3472

East Asian (EAS) AF: 0.884 AC: 4556 AN: 5152

South Asian (SAS) AF: 0.504 AC: 2425 AN: 4814

European-Finnish (FIN) AF: 0.597 AC: 6298 AN: 10552

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.587 AC: 39906 AN: 67950

Other (OTH) AF: 0.541 AC: 1141 AN: 2108

Alfa AF: 0.577 Hom.: 76749

Bravo AF: 0.546

Asia WGS AF: 0.705 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.34
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1555543; hg19: chr1-96944797;