chr1-220736824-A-G

Variant names:

• chr1-220736824-A-G
• rs337164

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 0.377 in 152,016 control chromosomes in the GnomAD database, including 13,935 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 (13935 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 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: 0.377 AC: 57273 AN: 151898 Hom.: 13890 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.377 AC: 57374 AN: 152016 Hom.: 13935 Cov.: 32 AF XY: 0.380 AC XY: 28255 AN XY: 74300

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.341

Alfa AF: 0.313 Hom.: 1191

Bravo AF: 0.408

Asia WGS AF: 0.545 AC: 1891 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	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs337164; hg19: chr1-220910166;