chr7-3070425-C-T

Variant names:

• chr7-3070425-C-T
• rs7805247

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.973 AC: 40420 AN: 41562

American (AMR) AF: 0.900 AC: 13771 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3084 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5183 AN: 5184

South Asian (SAS) AF: 0.959 AC: 4624 AN: 4824

European-Finnish (FIN) AF: 0.789 AC: 8338 AN: 10562

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57113 AN: 68014

Other (OTH) AF: 0.875 AC: 1850 AN: 2114

Alfa AF: 0.869 Hom.: 34123

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7805247; hg19: chr7-3110059;