rs4390300

Variant names:

• chr10-58384447-G-A
• rs4390300

Your query was ambiguous. Multiple possible variants found:

• chr10-58384447-G-A
• chr10-58384447-G-C
• chr10-58384447-G-T

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 0.556 in 152,054 control chromosomes in the GnomAD database, including 25,194 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 0.56 (25194 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) 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: 0.556 AC: 84448 AN: 151936 Hom.: 25161 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.556 AC: 84531 AN: 152054 Hom.: 25194 Cov.: 32 AF XY: 0.547 AC XY: 40654 AN XY: 74330

African (AFR) AF: 0.791 AC: 32837 AN: 41512

American (AMR) AF: 0.475 AC: 7266 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1920 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2525 AN: 5160

South Asian (SAS) AF: 0.430 AC: 2069 AN: 4816

European-Finnish (FIN) AF: 0.382 AC: 4031 AN: 10562

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32052 AN: 67934

Other (OTH) AF: 0.546 AC: 1150 AN: 2106

Alfa AF: 0.515 Hom.: 5199

Bravo AF: 0.575

Asia WGS AF: 0.439 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs4390300; hg19: chr10-60144207;