1-211320231-A-G

Variant names:

• chr1-211320231-A-G
• rs6540681

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 0.839 in 152,154 control chromosomes in the GnomAD database, including 53,622 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 0.84 (53622 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.941 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: 0.839 AC: 127580 AN: 152036 Hom.: 53585 Cov.: 31

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.839 AC: 127672 AN: 152154 Hom.: 53622 Cov.: 31 AF XY: 0.840 AC XY: 62476 AN XY: 74384

African (AFR) AF: 0.825 AC: 34235 AN: 41502

American (AMR) AF: 0.880 AC: 13457 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2809 AN: 3468

East Asian (EAS) AF: 0.963 AC: 4997 AN: 5188

South Asian (SAS) AF: 0.787 AC: 3787 AN: 4814

European-Finnish (FIN) AF: 0.846 AC: 8949 AN: 10578

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56763 AN: 67996

Other (OTH) AF: 0.823 AC: 1738 AN: 2112

Alfa AF: 0.837 Hom.: 67829

Bravo AF: 0.841

Asia WGS AF: 0.842 AC: 2925 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	1.9
DANN	Benign	0.69
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs6540681; hg19: chr1-211493573;