1-205085751-A-C

Variant names:

• chr1-205085751-A-C
• rs12139373

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 0.327 in 145,382 control chromosomes in the GnomAD database, including 9,092 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 0.33 (9092 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 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: 0.327 AC: 47489 AN: 145314 Hom.: 9093 Cov.: 30

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.327 AC: 47494 AN: 145382 Hom.: 9092 Cov.: 30 AF XY: 0.320 AC XY: 22561 AN XY: 70510

African (AFR) AF: 0.155 AC: 6212 AN: 40128

American (AMR) AF: 0.311 AC: 4489 AN: 14452

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1299 AN: 3402

East Asian (EAS) AF: 0.0478 AC: 223 AN: 4668

South Asian (SAS) AF: 0.135 AC: 594 AN: 4398

European-Finnish (FIN) AF: 0.444 AC: 3964 AN: 8920

Middle Eastern (MID) AF: 0.280 AC: 74 AN: 264

European-Non Finnish (NFE) AF: 0.447 AC: 29640 AN: 66270

Other (OTH) AF: 0.358 AC: 719 AN: 2008

Alfa AF: 0.394 Hom.: 5961

Bravo AF: 0.304

Asia WGS AF: 0.0730 AC: 256 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.98
DANN	Benign	0.48
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs12139373; hg19: chr1-205054879;