rs1467328

chr7-64290823-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_927595.2(LOC105375323):n.246+1194G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

LOC105375323 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375323	XR_927595.2	n.246+1194G>A		intron_variant, non_coding_transcript_variant
LOC105375323	XR_927597.2	n.246+1194G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.484

Alfa AF: 0.537 Hom.: 20036

Bravo AF: 0.496

Asia WGS AF: 0.383 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.5
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1467328; hg19: chr7-63751201;