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
• Publications: 0 publications found

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

African (AFR) AF: 0.269 AC: 8279 AN: 30782

American (AMR) AF: 0.250 AC: 3409 AN: 13634

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 472 AN: 3162

East Asian (EAS) AF: 0.453 AC: 2233 AN: 4930

South Asian (SAS) AF: 0.175 AC: 675 AN: 3864

European-Finnish (FIN) AF: 0.128 AC: 1263 AN: 9886

Middle Eastern (MID) AF: 0.205 AC: 50 AN: 244

European-Non Finnish (NFE) AF: 0.171 AC: 10828 AN: 63250

Other (OTH) AF: 0.205 AC: 370 AN: 1808

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
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs446713; hg19: chr1-196781876;