chr1-244347874-G-A

Variant names:

• chr1-244347874-G-A
• rs4658627

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 0.241 in 152,090 control chromosomes in the GnomAD database, including 4,703 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 0.24 (4703 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 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: 0.241 AC: 36666 AN: 151972 Hom.: 4708 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.0510

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.241 AC: 36681 AN: 152090 Hom.: 4703 Cov.: 33 AF XY: 0.239 AC XY: 17779 AN XY: 74364

African (AFR) AF: 0.211 AC: 8740 AN: 41446

American (AMR) AF: 0.225 AC: 3441 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1188 AN: 3468

East Asian (EAS) AF: 0.0501 AC: 260 AN: 5188

South Asian (SAS) AF: 0.238 AC: 1147 AN: 4820

European-Finnish (FIN) AF: 0.230 AC: 2429 AN: 10580

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18501 AN: 67988

Other (OTH) AF: 0.281 AC: 595 AN: 2114

Alfa AF: 0.267 Hom.: 23010

Bravo AF: 0.240

Asia WGS AF: 0.176 AC: 611 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.54
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs4658627; hg19: chr1-244511176;