1-21352107-T-G

Variant names:

• chr1-21352107-T-G
• rs213006

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 0.332 in 152,002 control chromosomes in the GnomAD database, including 8,678 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 0.33 (8678 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.373 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: 0.332 AC: 50467 AN: 151884 Hom.: 8661 Cov.: 31

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.332 AC: 50526 AN: 152002 Hom.: 8678 Cov.: 31 AF XY: 0.339 AC XY: 25151 AN XY: 74300

African (AFR) AF: 0.378 AC: 15671 AN: 41442

American (AMR) AF: 0.338 AC: 5163 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3470

East Asian (EAS) AF: 0.126 AC: 650 AN: 5174

South Asian (SAS) AF: 0.385 AC: 1853 AN: 4818

European-Finnish (FIN) AF: 0.377 AC: 3986 AN: 10574

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20859 AN: 67946

Other (OTH) AF: 0.337 AC: 709 AN: 2106

Alfa AF: 0.309 Hom.: 12772

Bravo AF: 0.325

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.39
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs213006; hg19: chr1-21678600;