1-188456478-T-C

Variant names:

• chr1-188456478-T-C
• rs957553

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 0.257 in 151,922 control chromosomes in the GnomAD database, including 5,238 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 0.26 (5238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.778
• 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 (SAS) allele frequency at 95% confidence interval = 0.399 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: 0.257 AC: 39029 AN: 151804 Hom.: 5227 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.257 AC: 39057 AN: 151922 Hom.: 5238 Cov.: 32 AF XY: 0.256 AC XY: 19016 AN XY: 74242

African (AFR) AF: 0.239 AC: 9896 AN: 41460

American (AMR) AF: 0.201 AC: 3064 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3464

East Asian (EAS) AF: 0.213 AC: 1098 AN: 5162

South Asian (SAS) AF: 0.414 AC: 2001 AN: 4830

European-Finnish (FIN) AF: 0.280 AC: 2944 AN: 10526

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18345 AN: 67924

Other (OTH) AF: 0.248 AC: 525 AN: 2114

Alfa AF: 0.259 Hom.: 934

Bravo AF: 0.245

Asia WGS AF: 0.353 AC: 1229 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	5.3
DANN	Benign	0.75
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs957553; hg19: chr1-188425609;