rs7078219

Variant names:

• chr10-99514608-G-A
• rs7078219

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 0.379 in 152,036 control chromosomes in the GnomAD database, including 11,343 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 (11343 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 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: 0.379 AC: 57566 AN: 151918 Hom.: 11320 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.379 AC: 57633 AN: 152036 Hom.: 11343 Cov.: 33 AF XY: 0.386 AC XY: 28701 AN XY: 74280

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.361

Alfa AF: 0.387 Hom.: 23912

Bravo AF: 0.377

Asia WGS AF: 0.435 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.9
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7078219; hg19: chr10-101274365;