chr1-228003664-G-A

Position:

• chr1-228003664-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 0.489 in 151,974 control chromosomes in the GnomAD database, including 18,617 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 0.49 (18617 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 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: 0.489 AC: 74235 AN: 151856 Hom.: 18609 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.489 AC: 74272 AN: 151974 Hom.: 18617 Cov.: 32 AF XY: 0.493 AC XY: 36622 AN XY: 74274

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.509

Alfa AF: 0.508 Hom.: 2494

Bravo AF: 0.473

Asia WGS AF: 0.580 AC: 2019 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	1.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs708111; hg19: chr1-228191365;