1-196812746-T-C

Variant names:

• chr1-196812746-T-C
• rs446713

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 0.21 in 132,440 control chromosomes in the GnomAD database, including 3,827 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 0.21 (3827 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 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: 0.210 AC: 27816 AN: 132316 Hom.: 3822 Cov.: 24

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.210 AC: 27828 AN: 132440 Hom.: 3827 Cov.: 24 AF XY: 0.209 AC XY: 13465 AN XY: 64400

Gnomad4 AFR AF: 0.269 AC: 0.268956 AN: 0.268956

Gnomad4 AMR AF: 0.250 AC: 0.250037 AN: 0.250037

Gnomad4 ASJ AF: 0.149 AC: 0.149273 AN: 0.149273

Gnomad4 EAS AF: 0.453 AC: 0.452941 AN: 0.452941

Gnomad4 SAS AF: 0.175 AC: 0.174689 AN: 0.174689

Gnomad4 FIN AF: 0.128 AC: 0.127756 AN: 0.127756

Gnomad4 NFE AF: 0.171 AC: 0.171194 AN: 0.171194

Gnomad4 OTH AF: 0.205 AC: 0.204646 AN: 0.204646

Alfa AF: 0.198 Hom.: 497

Asia WGS AF: 0.270 AC: 897 AN: 3320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs446713; hg19: chr1-196781876;