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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.550 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

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.541

Alfa AF: 0.584 Hom.: 33128

Bravo AF: 0.546

Asia WGS AF: 0.705 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555543; hg19: chr1-96944797;