7-68518718-A-G

Variant names:

• chr7-68518718-A-G
• rs10499801

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 0.0338 in 152,280 control chromosomes in the GnomAD database, including 125 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 0.034 (125 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0888 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: 0.0338 AC: 5143 AN: 152162 Hom.: 125 Cov.: 32

Gnomad AFR AF: 0.0362

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0110

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.0755

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0266

Gnomad OTH AF: 0.0263

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

GnomAD4 genome AF: 0.0338 AC: 5144 AN: 152280 Hom.: 125 Cov.: 32 AF XY: 0.0354 AC XY: 2634 AN XY: 74454

African (AFR) AF: 0.0363 AC: 1507 AN: 41558

American (AMR) AF: 0.0110 AC: 168 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3468

East Asian (EAS) AF: 0.0957 AC: 495 AN: 5170

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4826

European-Finnish (FIN) AF: 0.0755 AC: 801 AN: 10610

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0266 AC: 1809 AN: 68032

Other (OTH) AF: 0.0256 AC: 54 AN: 2112

Alfa AF: 0.0297 Hom.: 116

Bravo AF: 0.0299

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.073
DANN	Benign	0.40
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs10499801; hg19: chr7-67983705; COSMIC: COSV69632230;