rs7530323

chr1-38435020-G-A

Variant summary

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

The XR_947210.3(LOC105378657):n.424+64976C>T 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 0.35 in 152,106 control chromosomes in the GnomAD database, including 9,804 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 0.35 (9804 hom., cov: 32)
• Consequence: LOC105378657 XR_947210.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815

Genes affected

LOC107984943 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984943	XR_001737993.2	n.405+6183C>T		intron_variant, non_coding_transcript_variant
LOC105378657	XR_947210.3	n.424+64976C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53272 AN: 151988 Hom.: 9804 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.350 AC: 53287 AN: 152106 Hom.: 9804 Cov.: 32 AF XY: 0.349 AC XY: 25978 AN XY: 74348

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.368

Alfa AF: 0.369 Hom.: 1793

Bravo AF: 0.337

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	8.0
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7530323; hg19: chr1-38900692;