rs164041

Positions:

• chr1-162378327-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.141 in 152,208 control chromosomes in the GnomAD database, including 1,792 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 0.14 (1792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

ACMG classification

Verdict is Benign. Variant got -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 = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21419 AN: 152090 Hom.: 1790 Cov.: 32

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.141 AC: 21425 AN: 152208 Hom.: 1792 Cov.: 32 AF XY: 0.140 AC XY: 10445 AN XY: 74422

Gnomad4 AFR AF: 0.0562

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.0645

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.184

Alfa AF: 0.174 Hom.: 335

Bravo AF: 0.133

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs164041; hg19: chr1-162348117;