rs6728178

chr2-20971074-G-Achr2-20971074-G-Cchr2-20971074-G-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 0.256 in 152,184 control chromosomes in the GnomAD database, including 5,842 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 0.26 (5842 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 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: 0.256 AC: 38897 AN: 152066 Hom.: 5845 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.256 AC: 38903 AN: 152184 Hom.: 5842 Cov.: 33 AF XY: 0.262 AC XY: 19502 AN XY: 74392

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.253

Alfa AF: 0.247 Hom.: 6319

Bravo AF: 0.250

Asia WGS AF: 0.586 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.4
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6728178; hg19: chr2-21193946;