rs816236

Positions:

• chr7-56138165-T-G

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 0.151 in 152,138 control chromosomes in the GnomAD database, including 1,992 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 (1992 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 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: 0.151 AC: 22923 AN: 152020 Hom.: 1991 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.151 AC: 22948 AN: 152138 Hom.: 1992 Cov.: 33 AF XY: 0.156 AC XY: 11574 AN XY: 74364

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.145

Alfa AF: 0.133 Hom.: 1337

Bravo AF: 0.148

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.8
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs816236; hg19: chr7-56205858;