rs7865244

Variant names:

• chr9-6715730-A-C
• rs7865244

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 0.588 in 152,088 control chromosomes in the GnomAD database, including 26,475 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 0.59 (26475 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 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: 0.588 AC: 89283 AN: 151968 Hom.: 26445 Cov.: 33

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.588 AC: 89358 AN: 152088 Hom.: 26475 Cov.: 33 AF XY: 0.582 AC XY: 43262 AN XY: 74356

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.582

Alfa AF: 0.588 Hom.: 17399

Bravo AF: 0.590

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7865244; hg19: chr9-6715730;