rs7072438

Positions:

• chr10-57253276-A-C

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 0.213 in 142,648 control chromosomes in the GnomAD database, including 3,364 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 0.21 (3364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 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: 0.213 AC: 30392 AN: 142544 Hom.: 3365 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.00228

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.213 AC: 30398 AN: 142648 Hom.: 3364 Cov.: 32 AF XY: 0.211 AC XY: 14687 AN XY: 69582

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.00228

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.217

Alfa AF: 0.244 Hom.: 4842

Bravo AF: 0.196

Asia WGS AF: 0.102 AC: 334 AN: 3286

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7072438; hg19: chr10-59013036;