1-53478364-T-G

Variant names:

• chr1-53478364-T-G
• rs734908

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 0.445 in 152,208 control chromosomes in the GnomAD database, including 20,285 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 0.44 (20285 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.85 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: 0.444 AC: 67599 AN: 152090 Hom.: 20231 Cov.: 33

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.445 AC: 67707 AN: 152208 Hom.: 20285 Cov.: 33 AF XY: 0.440 AC XY: 32772 AN XY: 74434

African (AFR) AF: 0.857 AC: 35617 AN: 41542

American (AMR) AF: 0.275 AC: 4212 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 954 AN: 3472

East Asian (EAS) AF: 0.539 AC: 2788 AN: 5172

South Asian (SAS) AF: 0.431 AC: 2079 AN: 4826

European-Finnish (FIN) AF: 0.241 AC: 2556 AN: 10594

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18443 AN: 67986

Other (OTH) AF: 0.403 AC: 850 AN: 2110

Alfa AF: 0.352 Hom.: 4292

Bravo AF: 0.463

Asia WGS AF: 0.503 AC: 1749 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	2.9
DANN	Benign	0.44
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs734908; hg19: chr1-53944037;