1-17305969-C-G

Variant names:

• chr1-17305969-C-G
• rs34324150

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 0.108 in 152,206 control chromosomes in the GnomAD database, including 1,196 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 0.11 (1196 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 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: 0.108 AC: 16401 AN: 152086 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.0895

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0521

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.108 AC: 16403 AN: 152206 Hom.: 1196 Cov.: 32 AF XY: 0.107 AC XY: 7997 AN XY: 74406

African (AFR) AF: 0.0340 AC: 1413 AN: 41540

American (AMR) AF: 0.0893 AC: 1366 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0523 AC: 252 AN: 4818

European-Finnish (FIN) AF: 0.172 AC: 1819 AN: 10586

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10627 AN: 67998

Other (OTH) AF: 0.105 AC: 222 AN: 2112

Alfa AF: 0.0582 Hom.: 96

Bravo AF: 0.0974

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.63
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs34324150; hg19: chr1-17632464; COSMIC: COSV64925257;