1-214716516-T-C

Variant names:

• chr1-214716516-T-C
• rs335555

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 0.611 in 152,024 control chromosomes in the GnomAD database, including 28,936 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 0.61 (28936 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 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: 0.611 AC: 92790 AN: 151906 Hom.: 28897 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.611 AC: 92886 AN: 152024 Hom.: 28936 Cov.: 32 AF XY: 0.616 AC XY: 45790 AN XY: 74300

African (AFR) AF: 0.686 AC: 28441 AN: 41474

American (AMR) AF: 0.666 AC: 10159 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1950 AN: 3466

East Asian (EAS) AF: 0.894 AC: 4624 AN: 5170

South Asian (SAS) AF: 0.717 AC: 3460 AN: 4826

European-Finnish (FIN) AF: 0.586 AC: 6182 AN: 10554

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36101 AN: 67958

Other (OTH) AF: 0.625 AC: 1321 AN: 2112

Alfa AF: 0.562 Hom.: 81191

Bravo AF: 0.619

Asia WGS AF: 0.802 AC: 2785 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.050
DANN	Benign	0.66
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs335555; hg19: chr1-214889859;