1-35222214-T-C

Variant names:

• chr1-35222214-T-C
• rs673604

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 0.267 in 151,998 control chromosomes in the GnomAD database, including 8,893 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 0.27 (8893 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 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: 0.266 AC: 40453 AN: 151880 Hom.: 8849 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0883

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.267 AC: 40563 AN: 151998 Hom.: 8893 Cov.: 32 AF XY: 0.270 AC XY: 20077 AN XY: 74312

African (AFR) AF: 0.553 AC: 22891 AN: 41412

American (AMR) AF: 0.329 AC: 5009 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3468

East Asian (EAS) AF: 0.646 AC: 3332 AN: 5156

South Asian (SAS) AF: 0.206 AC: 994 AN: 4826

European-Finnish (FIN) AF: 0.129 AC: 1368 AN: 10592

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0883 AC: 6002 AN: 67992

Other (OTH) AF: 0.244 AC: 515 AN: 2110

Alfa AF: 0.147 Hom.: 14893

Bravo AF: 0.299

Asia WGS AF: 0.430 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.1
DANN	Benign	0.49
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs673604; hg19: chr1-35687815; COSMIC: COSV53316574;