chr1-201454954-A-G

Variant names:

• chr1-201454954-A-G
• rs3888929

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 0.618 in 151,968 control chromosomes in the GnomAD database, including 30,145 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 0.62 (30145 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.704 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: 0.618 AC: 93895 AN: 151848 Hom.: 30115 Cov.: 31

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.618 AC: 93984 AN: 151968 Hom.: 30145 Cov.: 31 AF XY: 0.608 AC XY: 45181 AN XY: 74268

African (AFR) AF: 0.557 AC: 23036 AN: 41392

American (AMR) AF: 0.582 AC: 8877 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2328 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1224 AN: 5186

South Asian (SAS) AF: 0.473 AC: 2278 AN: 4818

European-Finnish (FIN) AF: 0.558 AC: 5883 AN: 10550

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48224 AN: 67978

Other (OTH) AF: 0.613 AC: 1295 AN: 2112

Alfa AF: 0.633 Hom.: 5899

Bravo AF: 0.616

Asia WGS AF: 0.380 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.39
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs3888929; hg19: chr1-201424082;