1-226354348-A-G

Variant names:

• chr1-226354348-A-G
• rs6426551

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 0.734 in 152,050 control chromosomes in the GnomAD database, including 41,336 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 0.73 (41336 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.784 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: 0.734 AC: 111524 AN: 151932 Hom.: 41333 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.734 AC: 111572 AN: 152050 Hom.: 41336 Cov.: 31 AF XY: 0.728 AC XY: 54078 AN XY: 74306

African (AFR) AF: 0.775 AC: 32124 AN: 41458

American (AMR) AF: 0.629 AC: 9612 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2754 AN: 3466

East Asian (EAS) AF: 0.524 AC: 2710 AN: 5172

South Asian (SAS) AF: 0.805 AC: 3881 AN: 4820

European-Finnish (FIN) AF: 0.651 AC: 6872 AN: 10552

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51115 AN: 67998

Other (OTH) AF: 0.737 AC: 1557 AN: 2114

Alfa AF: 0.743 Hom.: 178636

Bravo AF: 0.732

Asia WGS AF: 0.690 AC: 2396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.59
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6426551; hg19: chr1-226542049;