rs568035

Variant names:

• chr1-156140376-C-T
• rs568035

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 0.224 in 151,964 control chromosomes in the GnomAD database, including 8,177 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 0.22 (8177 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) 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: 0.223 AC: 33909 AN: 151848 Hom.: 8137 Cov.: 31

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0228

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0566

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.224 AC: 33998 AN: 151964 Hom.: 8177 Cov.: 31 AF XY: 0.219 AC XY: 16264 AN XY: 74292

African (AFR) AF: 0.610 AC: 25234 AN: 41354

American (AMR) AF: 0.108 AC: 1647 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3470

East Asian (EAS) AF: 0.0226 AC: 117 AN: 5174

South Asian (SAS) AF: 0.127 AC: 611 AN: 4804

European-Finnish (FIN) AF: 0.0566 AC: 600 AN: 10596

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.0708 AC: 4813 AN: 67982

Other (OTH) AF: 0.180 AC: 379 AN: 2106

Alfa AF: 0.161 Hom.: 623

Bravo AF: 0.243

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.40
DANN	Benign	0.61
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs568035; hg19: chr1-156110167;