rs6960379

Variant names:

• chr7-64290139-T-C
• rs6960379
• XR_001745021.1:n.52A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745021.1(LOC105375323):​n.52A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 151,870 control chromosomes in the GnomAD database, including 3,461 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 0.15 (3461 hom., cov: 33)
• Consequence: LOC105375323 XR_001745021.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 3 publications found

Genes affected

LOC105375323 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21983 AN: 151748 Hom.: 3436 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.0683

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000590

Gnomad SAS AF: 0.0135

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.0769

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.145 AC: 22048 AN: 151870 Hom.: 3461 Cov.: 33 AF XY: 0.140 AC XY: 10387 AN XY: 74224

African (AFR) AF: 0.394 AC: 16317 AN: 41416

American (AMR) AF: 0.0682 AC: 1041 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 395 AN: 3466

East Asian (EAS) AF: 0.000591 AC: 3 AN: 5074

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4800

European-Finnish (FIN) AF: 0.0256 AC: 271 AN: 10606

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.0535 AC: 3637 AN: 67938

Other (OTH) AF: 0.116 AC: 246 AN: 2112

Alfa AF: 0.0885 Hom.: 813

Bravo AF: 0.160

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.2
DANN	Benign	0.65
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6960379; hg19: chr7-63750517;