chr6-120742550-A-C

Variant names:

• chr6-120742550-A-C
• rs1339014

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.649 AC: 26913 AN: 41458

American (AMR) AF: 0.944 AC: 14421 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3338 AN: 3472

East Asian (EAS) AF: 0.844 AC: 4357 AN: 5164

South Asian (SAS) AF: 0.953 AC: 4599 AN: 4828

European-Finnish (FIN) AF: 0.990 AC: 10521 AN: 10628

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.981 AC: 66712 AN: 68010

Other (OTH) AF: 0.904 AC: 1912 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	15
DANN	Benign	0.55
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1339014; hg19: chr6-121063696;