rs7272911

Positions:

• chr20-37317836-G-A
• chr20-37317836-G-C

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 0.327 in 152,024 control chromosomes in the GnomAD database, including 8,754 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 0.33 (8754 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37317836G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49646 AN: 151904 Hom.: 8741 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.327 AC: 49694 AN: 152024 Hom.: 8754 Cov.: 32 AF XY: 0.319 AC XY: 23711 AN XY: 74294

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.316

Alfa AF: 0.301 Hom.: 10638

Bravo AF: 0.334

Asia WGS AF: 0.268 AC: 935 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	2.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7272911; hg19: chr20-35946239;