chr1-106912668-G-A

Variant names:

• chr1-106912668-G-A
• rs4304614

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 0.568 in 152,016 control chromosomes in the GnomAD database, including 26,036 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 0.57 (26036 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 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: 0.569 AC: 86364 AN: 151896 Hom.: 26026 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.568 AC: 86412 AN: 152016 Hom.: 26036 Cov.: 32 AF XY: 0.572 AC XY: 42516 AN XY: 74300

African (AFR) AF: 0.361 AC: 14971 AN: 41454

American (AMR) AF: 0.619 AC: 9461 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3468

East Asian (EAS) AF: 0.664 AC: 3427 AN: 5158

South Asian (SAS) AF: 0.471 AC: 2270 AN: 4822

European-Finnish (FIN) AF: 0.773 AC: 8162 AN: 10558

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43956 AN: 67966

Other (OTH) AF: 0.572 AC: 1207 AN: 2110

Alfa AF: 0.612 Hom.: 92563

Bravo AF: 0.550

Asia WGS AF: 0.569 AC: 1978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.4
DANN	Benign	0.41
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs4304614; hg19: chr1-107455290;