chr7-124705304-C-G

Variant names:

• chr7-124705304-C-G
• rs1100508

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 0.57 in 151,530 control chromosomes in the GnomAD database, including 25,056 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 0.57 (25056 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86249 AN: 151412 Hom.: 25019 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.570 AC: 86332 AN: 151530 Hom.: 25056 Cov.: 31 AF XY: 0.568 AC XY: 42015 AN XY: 74006

African (AFR) AF: 0.690 AC: 28558 AN: 41368

American (AMR) AF: 0.551 AC: 8386 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1890 AN: 3462

East Asian (EAS) AF: 0.600 AC: 3089 AN: 5146

South Asian (SAS) AF: 0.564 AC: 2712 AN: 4808

European-Finnish (FIN) AF: 0.481 AC: 5052 AN: 10502

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.513 AC: 34761 AN: 67726

Other (OTH) AF: 0.580 AC: 1222 AN: 2108

Alfa AF: 0.369 Hom.: 811

Bravo AF: 0.582

Asia WGS AF: 0.597 AC: 2071 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.35
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1100508; hg19: chr7-124345358;