1-220741578-G-T

Variant names:

• chr1-220741578-G-T
• rs337161

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 0.237 in 151,886 control chromosomes in the GnomAD database, including 4,688 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 0.24 (4688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 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: 0.236 AC: 35868 AN: 151766 Hom.: 4669 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.237 AC: 35923 AN: 151886 Hom.: 4688 Cov.: 32 AF XY: 0.242 AC XY: 17981 AN XY: 74216

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.234

Alfa AF: 0.206 Hom.: 4776

Bravo AF: 0.250

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs337161; hg19: chr1-220914920;