rs1890645

Variant names:

• chr1-195562293-T-C
• rs1890645

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 0.332 in 152,014 control chromosomes in the GnomAD database, including 8,553 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 (8553 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.412 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: 0.332 AC: 50379 AN: 151896 Hom.: 8532 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.332 AC: 50446 AN: 152014 Hom.: 8553 Cov.: 32 AF XY: 0.337 AC XY: 25029 AN XY: 74322

African (AFR) AF: 0.332 AC: 13782 AN: 41472

American (AMR) AF: 0.421 AC: 6425 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3466

East Asian (EAS) AF: 0.311 AC: 1607 AN: 5164

South Asian (SAS) AF: 0.316 AC: 1523 AN: 4814

European-Finnish (FIN) AF: 0.340 AC: 3593 AN: 10560

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21750 AN: 67960

Other (OTH) AF: 0.311 AC: 657 AN: 2114

Alfa AF: 0.320 Hom.: 37032

Bravo AF: 0.340

Asia WGS AF: 0.336 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.44
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs1890645; hg19: chr1-195531423; COSMIC: COSV60011044;