rs7727306

Positions:

• chr5-35237758-C-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 0.317 in 152,058 control chromosomes in the GnomAD database, including 8,695 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 0.32 (8695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 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: 0.317 AC: 48123 AN: 151940 Hom.: 8691 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.0904

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.317 AC: 48128 AN: 152058 Hom.: 8695 Cov.: 32 AF XY: 0.318 AC XY: 23625 AN XY: 74328

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.0904

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.344

Alfa AF: 0.385 Hom.: 6729

Bravo AF: 0.297

Asia WGS AF: 0.297 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7727306; hg19: chr5-35237860;