10-6064589-T-C

Variant names:

• chr10-6064589-T-C
• rs7073236

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 0.451 in 152,036 control chromosomes in the GnomAD database, including 15,839 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 0.45 (15839 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.761
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 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: 0.451 AC: 68508 AN: 151918 Hom.: 15811 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.451 AC: 68580 AN: 152036 Hom.: 15839 Cov.: 31 AF XY: 0.459 AC XY: 34127 AN XY: 74310

African (AFR) AF: 0.440 AC: 18233 AN: 41480

American (AMR) AF: 0.532 AC: 8129 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3466

East Asian (EAS) AF: 0.560 AC: 2896 AN: 5174

South Asian (SAS) AF: 0.534 AC: 2573 AN: 4820

European-Finnish (FIN) AF: 0.544 AC: 5743 AN: 10566

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.420 AC: 28516 AN: 67946

Other (OTH) AF: 0.440 AC: 930 AN: 2112

Alfa AF: 0.431 Hom.: 7501

Bravo AF: 0.448

Asia WGS AF: 0.550 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.21
DANN	Benign	0.42
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs7073236; hg19: chr10-6106552;