rs4311892

Variant names:

• chr1-206738221-A-G
• rs4311892

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 0.265 in 152,210 control chromosomes in the GnomAD database, including 5,501 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 0.27 (5501 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 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: 0.265 AC: 40319 AN: 152092 Hom.: 5495 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.265 AC: 40354 AN: 152210 Hom.: 5501 Cov.: 33 AF XY: 0.274 AC XY: 20383 AN XY: 74410

African (AFR) AF: 0.207 AC: 8583 AN: 41526

American (AMR) AF: 0.353 AC: 5395 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 945 AN: 3468

East Asian (EAS) AF: 0.319 AC: 1649 AN: 5174

South Asian (SAS) AF: 0.471 AC: 2276 AN: 4828

European-Finnish (FIN) AF: 0.273 AC: 2892 AN: 10596

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17726 AN: 68012

Other (OTH) AF: 0.292 AC: 616 AN: 2106

Alfa AF: 0.271 Hom.: 6183

Bravo AF: 0.262

Asia WGS AF: 0.399 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.059
DANN	Benign	0.51
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs4311892; hg19: chr1-206911566;