1-220741578-G-T

Variant names:

• chr1-220741578-G-T
• rs337161

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 0.237 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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.262 AC: 10837 AN: 41422

American (AMR) AF: 0.316 AC: 4821 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3472

East Asian (EAS) AF: 0.468 AC: 2397 AN: 5126

South Asian (SAS) AF: 0.319 AC: 1533 AN: 4802

European-Finnish (FIN) AF: 0.209 AC: 2200 AN: 10538

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12517 AN: 67958

Other (OTH) AF: 0.234 AC: 495 AN: 2112

Alfa AF: 0.208 Hom.: 12759

Bravo AF: 0.250

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs337161; hg19: chr1-220914920;