chr1-172695302-A-G

Position:

• chr1-172695302-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.388 in 151,870 control chromosomes in the GnomAD database, including 12,911 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 0.39 (12911 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58837 AN: 151752 Hom.: 12901 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.00889

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.388 AC: 58871 AN: 151870 Hom.: 12911 Cov.: 31 AF XY: 0.380 AC XY: 28209 AN XY: 74256

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.00891

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.358

Alfa AF: 0.322 Hom.: 4699

Bravo AF: 0.399

Asia WGS AF: 0.151 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs859665; hg19: chr1-172664442; COSMIC: COSV56922091;