chr7-24067707-G-A

Variant names:

• chr7-24067707-G-A
• rs10216322

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 0.15 in 152,076 control chromosomes in the GnomAD database, including 2,219 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 0.15 (2219 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.204 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: 0.150 AC: 22837 AN: 151958 Hom.: 2219 Cov.: 31

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0843

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.150 AC: 22830 AN: 152076 Hom.: 2219 Cov.: 31 AF XY: 0.152 AC XY: 11266 AN XY: 74322

African (AFR) AF: 0.0514 AC: 2133 AN: 41490

American (AMR) AF: 0.125 AC: 1907 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3466

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5184

South Asian (SAS) AF: 0.0840 AC: 404 AN: 4810

European-Finnish (FIN) AF: 0.281 AC: 2967 AN: 10560

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14042 AN: 67976

Other (OTH) AF: 0.161 AC: 340 AN: 2108

Alfa AF: 0.187 Hom.: 1453

Bravo AF: 0.134

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.85
DANN	Benign	0.94
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs10216322; hg19: chr7-24107326;