rs59072263

Variant names:

• chr7-8112437-G-T
• rs59072263

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.209 AC: 8675 AN: 41458

American (AMR) AF: 0.128 AC: 1953 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3470

East Asian (EAS) AF: 0.0994 AC: 513 AN: 5162

South Asian (SAS) AF: 0.112 AC: 538 AN: 4816

European-Finnish (FIN) AF: 0.0779 AC: 826 AN: 10602

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9565 AN: 67964

Other (OTH) AF: 0.156 AC: 330 AN: 2110

Alfa AF: 0.147 Hom.: 2893

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
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs59072263; hg19: chr7-8152067;