7-3070425-C-T

Variant names:

• chr7-3070425-C-T
• rs7805247

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 0.889 in 152,230 control chromosomes in the GnomAD database, including 60,509 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 0.89 (60509 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.889 AC: 135187 AN: 152112 Hom.: 60440 Cov.: 31

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.889 AC: 135316 AN: 152230 Hom.: 60509 Cov.: 31 AF XY: 0.890 AC XY: 66228 AN XY: 74410

Gnomad4 AFR AF: 0.973

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.959

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.875

Alfa AF: 0.867 Hom.: 21668

Bravo AF: 0.897

Asia WGS AF: 0.978 AC: 3401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	10
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7805247; hg19: chr7-3110059;