rs10889697

Variant names:

• chr1-67496439-G-A
• rs10889697

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 0.138 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0525 AC: 2181 AN: 41524

American (AMR) AF: 0.172 AC: 2630 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3472

East Asian (EAS) AF: 0.00444 AC: 23 AN: 5182

South Asian (SAS) AF: 0.0828 AC: 399 AN: 4820

European-Finnish (FIN) AF: 0.176 AC: 1856 AN: 10554

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12918 AN: 67970

Other (OTH) AF: 0.127 AC: 269 AN: 2116

Alfa AF: 0.170 Hom.: 351

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10889697; hg19: chr1-67962122;