rs1338221

Variant names:

• chr1-219627563-T-C
• rs1338221

Your query was ambiguous. Multiple possible variants found:

• chr1-219627563-T-C
• chr1-219627563-T-G

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 0.759 in 152,004 control chromosomes in the GnomAD database, including 44,729 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 0.76 (44729 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 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: 0.759 AC: 115254 AN: 151886 Hom.: 44708 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.759 AC: 115321 AN: 152004 Hom.: 44729 Cov.: 32 AF XY: 0.762 AC XY: 56635 AN XY: 74304

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.770

Alfa AF: 0.806 Hom.: 27669

Bravo AF: 0.747

Asia WGS AF: 0.874 AC: 3042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.016
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1338221; hg19: chr1-219800905;