rs1467328

Variant names:

• chr7-64290823-C-T
• rs1467328
• XR_927595.2:n.246+1194G>A

Variant summary

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

The XR_927595.2(LOC105375323):​n.246+1194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 152,088 control chromosomes in the GnomAD database, including 19,934 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 0.50 (19934 hom., cov: 33)
• Consequence: LOC105375323 XR_927595.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76378 AN: 151970 Hom.: 19933 Cov.: 33

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.502 AC: 76390 AN: 152088 Hom.: 19934 Cov.: 33 AF XY: 0.504 AC XY: 37477 AN XY: 74366

African (AFR) AF: 0.399 AC: 16558 AN: 41492

American (AMR) AF: 0.575 AC: 8792 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1935 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1368 AN: 5154

South Asian (SAS) AF: 0.434 AC: 2096 AN: 4830

European-Finnish (FIN) AF: 0.618 AC: 6537 AN: 10586

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37299 AN: 67954

Other (OTH) AF: 0.484 AC: 1023 AN: 2114

Alfa AF: 0.532 Hom.: 25228

Bravo AF: 0.496

Asia WGS AF: 0.383 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.5
DANN	Benign	0.25
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1467328; hg19: chr7-63751201;