chr1-18629964-G-A

Position:

• chr1-18629964-G-A

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 0.581 in 152,096 control chromosomes in the GnomAD database, including 27,281 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 0.58 (27281 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 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: 0.581 AC: 88274 AN: 151978 Hom.: 27223 Cov.: 33

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.581 AC: 88396 AN: 152096 Hom.: 27281 Cov.: 33 AF XY: 0.579 AC XY: 43055 AN XY: 74326

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.570

Alfa AF: 0.539 Hom.: 10385

Bravo AF: 0.577

Asia WGS AF: 0.344 AC: 1197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs766325; hg19: chr1-18956458;