chr7-107021638-A-G

Variant names:

• chr7-107021638-A-G
• rs7798500

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 0.136 in 152,186 control chromosomes in the GnomAD database, including 2,905 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 0.14 (2905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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: 0.136 AC: 20727 AN: 152070 Hom.: 2896 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0683

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0493

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0507

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.136 AC: 20764 AN: 152186 Hom.: 2905 Cov.: 32 AF XY: 0.131 AC XY: 9746 AN XY: 74414

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.0681

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.0492

Gnomad4 SAS AF: 0.0299

Gnomad4 FIN AF: 0.0372

Gnomad4 NFE AF: 0.0506

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0627 Hom.: 1105

Bravo AF: 0.150

Asia WGS AF: 0.0610 AC: 213 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	1.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7798500; hg19: chr7-106662083;