rs10494891

Variant names:

• chr1-207180855-A-G
• rs10494891

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 0.0894 in 152,122 control chromosomes in the GnomAD database, including 1,456 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 0.089 (1456 hom., cov: 32)
• Consequence: C4BPAP1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.906
• Publications: 1 publications found

Genes affected

C4BPAP1 (HGNC:1326): (C4BPA pseudogene 1)

ENSG00000243636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415474.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C4BPAP1	ENST00000415474.1	TSL:6	n.1301-520A>G		intron	N/A
	ENSG00000243636	ENST00000442684.2	TSL:3	n.250-520A>G		intron	N/A
	ENSG00000296591	ENST00000740658.1		n.117-46075T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0891 AC: 13550 AN: 152004 Hom.: 1447 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0460

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00809

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0226

Gnomad OTH AF: 0.0745

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

GnomAD4 genome AF: 0.0894 AC: 13597 AN: 152122 Hom.: 1456 Cov.: 32 AF XY: 0.0871 AC XY: 6476 AN XY: 74356

African (AFR) AF: 0.258 AC: 10701 AN: 41428

American (AMR) AF: 0.0459 AC: 702 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00789 AC: 38 AN: 4818

European-Finnish (FIN) AF: 0.0362 AC: 384 AN: 10600

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0226 AC: 1536 AN: 68016

Other (OTH) AF: 0.0737 AC: 156 AN: 2116

Alfa AF: 0.0525 Hom.: 104

Bravo AF: 0.0992

Asia WGS AF: 0.0310 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.51
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs10494891; hg19: chr1-207354200;