rs7543757

Variant names:

• chr1-104685292-T-C
• rs7543757

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 0.457 in 152,124 control chromosomes in the GnomAD database, including 18,753 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 0.46 (18753 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 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: 0.458 AC: 69552 AN: 152006 Hom.: 18763 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.457 AC: 69546 AN: 152124 Hom.: 18753 Cov.: 32 AF XY: 0.458 AC XY: 34039 AN XY: 74364

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.420

Alfa AF: 0.567 Hom.: 50382

Bravo AF: 0.418

Asia WGS AF: 0.282 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7543757; hg19: chr1-105227914;