1-32290838-T-C

Variant names:

• chr1-32290838-T-C
• rs1741981

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 0.454 in 151,054 control chromosomes in the GnomAD database, including 18,753 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 0.45 (18753 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.996
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 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: 0.453 AC: 68415 AN: 150940 Hom.: 18704 Cov.: 28

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.352

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.454 AC: 68515 AN: 151054 Hom.: 18753 Cov.: 28 AF XY: 0.454 AC XY: 33445 AN XY: 73674

African (AFR) AF: 0.778 AC: 32050 AN: 41210

American (AMR) AF: 0.300 AC: 4541 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1537 AN: 3464

East Asian (EAS) AF: 0.491 AC: 2482 AN: 5056

South Asian (SAS) AF: 0.275 AC: 1318 AN: 4790

European-Finnish (FIN) AF: 0.420 AC: 4366 AN: 10392

Middle Eastern (MID) AF: 0.351 AC: 101 AN: 288

European-Non Finnish (NFE) AF: 0.310 AC: 20978 AN: 67742

Other (OTH) AF: 0.407 AC: 850 AN: 2090

Alfa AF: 0.352 Hom.: 28883

Bravo AF: 0.459

Asia WGS AF: 0.393 AC: 1369 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	3.0
DANN	Benign	0.75
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1741981; hg19: chr1-32756439;