1-19974051-A-G

Variant names:

• chr1-19974051-A-G
• rs10916683

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 0.145 in 152,298 control chromosomes in the GnomAD database, including 1,724 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 0.14 (1724 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.739
• Publications: 5 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 (AMR) allele frequency at 95% confidence interval = 0.193 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: 0.145 AC: 22054 AN: 152180 Hom.: 1724 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0475

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.145 AC: 22081 AN: 152298 Hom.: 1724 Cov.: 33 AF XY: 0.144 AC XY: 10757 AN XY: 74470

African (AFR) AF: 0.110 AC: 4570 AN: 41572

American (AMR) AF: 0.199 AC: 3045 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 730 AN: 3472

East Asian (EAS) AF: 0.0476 AC: 247 AN: 5188

South Asian (SAS) AF: 0.117 AC: 567 AN: 4826

European-Finnish (FIN) AF: 0.110 AC: 1165 AN: 10598

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11279 AN: 68022

Other (OTH) AF: 0.147 AC: 310 AN: 2114

Alfa AF: 0.162 Hom.: 7857

Bravo AF: 0.150

Asia WGS AF: 0.101 AC: 355 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	6.1
DANN	Benign	0.66
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs10916683; hg19: chr1-20300544;