1-162060898-C-G

Variant names:

• chr1-162060898-C-G
• rs10918594

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 0.38 in 152,088 control chromosomes in the GnomAD database, including 11,515 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 0.38 (11515 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 22 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 (SAS) allele frequency at 95% confidence interval = 0.63 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: 0.381 AC: 57835 AN: 151970 Hom.: 11514 Cov.: 33

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.380 AC: 57851 AN: 152088 Hom.: 11515 Cov.: 33 AF XY: 0.386 AC XY: 28671 AN XY: 74346

African (AFR) AF: 0.424 AC: 17575 AN: 41474

American (AMR) AF: 0.370 AC: 5659 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1333 AN: 3468

East Asian (EAS) AF: 0.533 AC: 2750 AN: 5164

South Asian (SAS) AF: 0.649 AC: 3127 AN: 4820

European-Finnish (FIN) AF: 0.355 AC: 3759 AN: 10586

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22396 AN: 67964

Other (OTH) AF: 0.378 AC: 799 AN: 2112

Alfa AF: 0.331 Hom.: 1084

Bravo AF: 0.376

Asia WGS AF: 0.585 AC: 2034 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	1.5
DANN	Benign	0.58
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs10918594; hg19: chr1-162030688;