rs727087

Positions:

• chr7-8431700-T-C

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 0.165 in 152,194 control chromosomes in the GnomAD database, including 2,311 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 0.17 (2311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

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 = 0.23 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: 0.165 AC: 25095 AN: 152076 Hom.: 2306 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0375

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.0989

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.165 AC: 25127 AN: 152194 Hom.: 2311 Cov.: 32 AF XY: 0.162 AC XY: 12036 AN XY: 74422

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.0374

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0989

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.178

Alfa AF: 0.166 Hom.: 377

Bravo AF: 0.167

Asia WGS AF: 0.121 AC: 418 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	1.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs727087; hg19: chr7-8471330;