rs7075697

Positions:

• chr10-46048451-C-G
• chr10-46048451-C-T

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 0.376 in 151,668 control chromosomes in the GnomAD database, including 11,181 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 0.38 (11181 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984

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 (SAS) allele frequency at 95% confidence interval = 0.503 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: 0.376 AC: 57013 AN: 151550 Hom.: 11172 Cov.: 30

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.376 AC: 57048 AN: 151668 Hom.: 11181 Cov.: 30 AF XY: 0.378 AC XY: 28043 AN XY: 74126

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.405

Alfa AF: 0.374 Hom.: 1321

Bravo AF: 0.367

Asia WGS AF: 0.486 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7075697; hg19: chr10-51547371;