rs10753578

Variant names:

• chr1-162552026-G-A
• rs10753578

Your query was ambiguous. Multiple possible variants found:

• chr1-162552026-G-A
• chr1-162552026-G-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 0.234 in 151,582 control chromosomes in the GnomAD database, including 4,367 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 0.23 (4367 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744

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 = 0.299 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: 0.234 AC: 35424 AN: 151488 Hom.: 4357 Cov.: 30

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.234 AC: 35472 AN: 151582 Hom.: 4367 Cov.: 30 AF XY: 0.237 AC XY: 17570 AN XY: 74046

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.264

Alfa AF: 0.227 Hom.: 4042

Bravo AF: 0.239

Asia WGS AF: 0.281 AC: 982 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	0.053
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10753578; hg19: chr1-162521816;