rs816236

Variant names:

• chr7-56138165-T-G
• rs816236

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;