chr7-89538067-C-A

Position:

• chr7-89538067-C-A

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 0.148 in 151,938 control chromosomes in the GnomAD database, including 1,815 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 (1815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22511 AN: 151822 Hom.: 1810 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0972

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.148 AC: 22549 AN: 151938 Hom.: 1815 Cov.: 32 AF XY: 0.145 AC XY: 10732 AN XY: 74254

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0969

Gnomad4 SAS AF: 0.0970

Gnomad4 FIN AF: 0.0851

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.148

Alfa AF: 0.102 Hom.: 261

Bravo AF: 0.159

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7787163; hg19: chr7-89167381; COSMIC: COSV50193138;