rs1339014

chr6-120742550-A-Cchr6-120742550-A-Gchr6-120742550-A-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 0.88 in 152,160 control chromosomes in the GnomAD database, including 60,560 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 0.88 (60560 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.975 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: 0.881 AC: 133894 AN: 152042 Hom.: 60551 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.880 AC: 133948 AN: 152160 Hom.: 60560 Cov.: 32 AF XY: 0.883 AC XY: 65706 AN XY: 74418

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.944

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.953

Gnomad4 FIN AF: 0.990

Gnomad4 NFE AF: 0.981

Gnomad4 OTH AF: 0.904

Alfa AF: 0.922 Hom.: 3778

Bravo AF: 0.866

Asia WGS AF: 0.874 AC: 3040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	15
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: rs1339014; hg19: chr6-121063696;