rs9348530

chr6-22656742-G-Achr6-22656742-G-Cchr6-22656742-G-T

Variant summary

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

The XR_007059495.1(LOC105374973):n.3350G>A 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 0.812 in 152,136 control chromosomes in the GnomAD database, including 50,533 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 0.81 (50533 hom., cov: 32)
• Consequence: LOC105374973 XR_007059495.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.532

Genes affected

LOC105374973 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374973	XR_007059495.1	n.3350G>A		non_coding_transcript_exon_variant	4/4
LINC03005	NR_134614.1	n.249+10253C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123408 AN: 152018 Hom.: 50491 Cov.: 32

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.812 AC: 123507 AN: 152136 Hom.: 50533 Cov.: 32 AF XY: 0.813 AC XY: 60456 AN XY: 74364

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.802

Alfa AF: 0.796 Hom.: 8163

Bravo AF: 0.823

Asia WGS AF: 0.735 AC: 2559 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	5.2
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9348530; hg19: chr6-22656971;