chr7-99785313-A-G

Variant names:

• chr7-99785313-A-G
• rs1851426

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 0.779 in 152,212 control chromosomes in the GnomAD database, including 52,519 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 0.78 (52519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.780 AC: 118585 AN: 152094 Hom.: 52518 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.779 AC: 118606 AN: 152212 Hom.: 52519 Cov.: 32 AF XY: 0.786 AC XY: 58540 AN XY: 74436

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.970

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.965

Gnomad4 OTH AF: 0.828

Alfa AF: 0.874 Hom.: 23534

Bravo AF: 0.751

Asia WGS AF: 0.936 AC: 3253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1851426; hg19: chr7-99382936;