rs7543757

Variant names:

• chr1-104685292-T-C
• rs7543757

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 0.457 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
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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

African (AFR) AF: 0.204 AC: 8469 AN: 41504

American (AMR) AF: 0.386 AC: 5890 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1952 AN: 3472

East Asian (EAS) AF: 0.178 AC: 921 AN: 5180

South Asian (SAS) AF: 0.375 AC: 1811 AN: 4830

European-Finnish (FIN) AF: 0.719 AC: 7607 AN: 10584

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41360 AN: 67974

Other (OTH) AF: 0.420 AC: 883 AN: 2104

Alfa AF: 0.550 Hom.: 101856

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7543757; hg19: chr1-105227914;