rs10889697

Positions:

• chr1-67496439-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;