rs6753321

chr2-138858309-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;