rs10489072

Variant names:

• chr4-10271620-T-C
• rs10489072

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 0.697 in 151,676 control chromosomes in the GnomAD database, including 37,217 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 0.70 (37217 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.722 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: 0.697 AC: 105603 AN: 151558 Hom.: 37177 Cov.: 30

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.697 AC: 105695 AN: 151676 Hom.: 37217 Cov.: 30 AF XY: 0.695 AC XY: 51486 AN XY: 74078

African (AFR) AF: 0.729 AC: 30183 AN: 41400

American (AMR) AF: 0.690 AC: 10537 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2782 AN: 3468

East Asian (EAS) AF: 0.516 AC: 2637 AN: 5112

South Asian (SAS) AF: 0.737 AC: 3508 AN: 4758

European-Finnish (FIN) AF: 0.658 AC: 6869 AN: 10446

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46859 AN: 67912

Other (OTH) AF: 0.715 AC: 1508 AN: 2110

Alfa AF: 0.703 Hom.: 39740

Bravo AF: 0.701

Asia WGS AF: 0.647 AC: 2247 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.3
DANN	Benign	0.34
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10489072; hg19: chr4-10273244;