6-1524335-G-C

Variant summary

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

The XR_427861.4(LOC102723944):n.235-21772C>G 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 0.0842 in 152,342 control chromosomes in the GnomAD database, including 567 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 0.084 (567 hom., cov: 32)
• Consequence: LOC102723944 XR_427861.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195

Genes affected

LOC102723944 (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 (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723944	XR_427861.4	n.235-21772C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0841 AC: 12809 AN: 152222 Hom.: 567 Cov.: 32

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0690

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0579

Gnomad FIN AF: 0.0616

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.0840

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

GnomAD4 genome AF: 0.0842 AC: 12822 AN: 152342 Hom.: 567 Cov.: 32 AF XY: 0.0826 AC XY: 6156 AN XY: 74492

Gnomad4 AFR AF: 0.0717

Gnomad4 AMR AF: 0.0689

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0592

Gnomad4 FIN AF: 0.0616

Gnomad4 NFE AF: 0.0930

Gnomad4 OTH AF: 0.0827

Alfa AF: 0.0313 Hom.: 24

Bravo AF: 0.0860

Asia WGS AF: 0.0880 AC: 305 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	4.9
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2569872; hg19: chr6-1524570;