rs6753321

Variant names:

• chr2-138858309-T-C
• rs6753321

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0947 in 152,196 control chromosomes in the GnomAD database, including 797 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 0.095 (797 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.09

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 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: 0.0947 AC: 14405 AN: 152078 Hom.: 794 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0699

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.0692

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0842

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0947 AC: 14410 AN: 152196 Hom.: 797 Cov.: 32 AF XY: 0.0925 AC XY: 6880 AN XY: 74416

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0698

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.0692

Gnomad4 NFE AF: 0.0842

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0874 Hom.: 337

Bravo AF: 0.0964

Asia WGS AF: 0.0300 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6753321; hg19: chr2-139615879;