rs59072263

Positions:

• chr7-8112437-G-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 0.152 in 152,076 control chromosomes in the GnomAD database, including 1,910 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 (1910 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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: 0.152 AC: 23067 AN: 151958 Hom.: 1906 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.152 AC: 23084 AN: 152076 Hom.: 1910 Cov.: 31 AF XY: 0.146 AC XY: 10853 AN XY: 74342

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0994

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0779

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.156

Alfa AF: 0.144 Hom.: 350

Bravo AF: 0.161

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs59072263; hg19: chr7-8152067;