chr7-89431419-C-T

Position:

• chr7-89431419-C-T

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 0.164 in 152,088 control chromosomes in the GnomAD database, including 3,270 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 0.16 (3270 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24817 AN: 151970 Hom.: 3254 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.0781

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.164 AC: 24882 AN: 152088 Hom.: 3270 Cov.: 32 AF XY: 0.160 AC XY: 11896 AN XY: 74366

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0354

Gnomad4 NFE AF: 0.0781

Gnomad4 OTH AF: 0.185

Alfa AF: 0.125 Hom.: 317

Bravo AF: 0.181

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6973392; hg19: chr7-89060733;