rs7072438

Variant names:

• chr10-57253276-A-C
• rs7072438

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;