rs396038

Positions:

• chr6-31305203-C-T

Variant summary

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

The XR_926691.3(LOC112267902):​n.964+1575G>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 0.104 in 152,246 control chromosomes in the GnomAD database, including 925 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 0.10 (925 hom., cov: 32)
• Consequence: LOC112267902 XR_926691.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

LOC112267902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3	n.964+1575G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15893 AN: 152128 Hom.: 926 Cov.: 32

Gnomad AFR AF: 0.0781

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0745

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.104 AC: 15893 AN: 152246 Hom.: 925 Cov.: 32 AF XY: 0.0992 AC XY: 7382 AN XY: 74430

Gnomad4 AFR AF: 0.0779

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0741

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0985 Hom.: 337

Bravo AF: 0.110

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs396038; hg19: chr6-31272980;