rs10916407

Variant names:

• chr1-229014074-G-A
• rs10916407

Your query was ambiguous. Multiple possible variants found:

• chr1-229014074-G-A
• chr1-229014074-G-T

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 0.293 in 143,464 control chromosomes in the GnomAD database, including 6,735 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 0.29 (6735 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 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: 0.293 AC: 42037 AN: 143352 Hom.: 6728 Cov.: 27

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.293 AC: 42071 AN: 143464 Hom.: 6735 Cov.: 27 AF XY: 0.304 AC XY: 20926 AN XY: 68894

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.302

Alfa AF: 0.257 Hom.: 2704

Bravo AF: 0.291

Asia WGS AF: 0.581 AC: 2019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	7.1
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10916407; hg19: chr1-229149821;