rs6728178

Variant names:

• chr2-20971074-G-A
• rs6728178

Your query was ambiguous. Multiple possible variants found:

• chr2-20971074-G-A
• chr2-20971074-G-C
• chr2-20971074-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;