rs4304614

Positions:

• chr1-106912668-G-A
• chr1-106912668-G-C

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 0.568 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.572

Alfa AF: 0.626 Hom.: 60709

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4304614; hg19: chr1-107455290;