rs3800307

chr6-27218013-T-A

Variant summary

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

The XR_007059536.1(LOC124901293):n.204-84T>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 0.159 in 151,776 control chromosomes in the GnomAD database, including 2,103 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 0.16 (2103 hom., cov: 31)
• Consequence: LOC124901293 XR_007059536.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

Genes affected

LOC124901293 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901293	XR_007059536.1	n.204-84T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24101 AN: 151658 Hom.: 2103 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0190

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.159 AC: 24102 AN: 151776 Hom.: 2103 Cov.: 31 AF XY: 0.152 AC XY: 11245 AN XY: 74148

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.0188

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.149

Alfa AF: 0.175 Hom.: 306

Bravo AF: 0.161

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.5
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3800307; hg19: chr6-27185792;