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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375323	XR_001745021.1	n.52A>G		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105375323	XR_927595.2	n.247-583A>G		intron_variant	Intron 1 of 3
LOC105375323	XR_927597.2	n.247-583A>G		intron_variant	Intron 1 of 3
LOC105375323	XR_001745020.1	n.-217A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;