rs10889697

Variant names:

• chr1-67496439-G-A
• rs10889697

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 0.138 in 152,108 control chromosomes in the GnomAD database, including 1,833 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 0.14 (1833 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.187 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: 0.138 AC: 20909 AN: 151990 Hom.: 1833 Cov.: 31

Gnomad AFR AF: 0.0525

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.0817

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.138 AC: 20919 AN: 152108 Hom.: 1833 Cov.: 31 AF XY: 0.135 AC XY: 10048 AN XY: 74354

Gnomad4 AFR AF: 0.0525

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.0828

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.127

Alfa AF: 0.175 Hom.: 350

Bravo AF: 0.132

Asia WGS AF: 0.0710 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10889697; hg19: chr1-67962122;