rs4140564

Variant names:

• chr1-186755871-G-A
• rs4140564

Your query was ambiguous. Multiple possible variants found:

• chr1-186755871-G-A
• chr1-186755871-G-C
• chr1-186755871-G-T

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 0.935 in 150,752 control chromosomes in the GnomAD database, including 65,878 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 0.93 (65878 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.935 AC: 140812 AN: 150638 Hom.: 65826 Cov.: 25

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.935 AC: 140919 AN: 150752 Hom.: 65878 Cov.: 25 AF XY: 0.936 AC XY: 68783 AN XY: 73456

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.971

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.931

Gnomad4 FIN AF: 0.923

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.944

Alfa AF: 0.945 Hom.: 115344

Bravo AF: 0.938

Asia WGS AF: 0.966 AC: 3359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4140564; hg19: chr1-186725003;