rs10484978

chr6-84360679-G-A

Variant summary

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

The XR_001744235.2(LOC107986620):n.130+7758G>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 0.113 in 151,996 control chromosomes in the GnomAD database, including 1,020 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 0.11 (1020 hom., cov: 33)
• Consequence: LOC107986620 XR_001744235.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

Genes affected

LOC107986620 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986620	XR_001744235.2	n.130+7758G>A		intron_variant, non_coding_transcript_variant
LOC107986621	XR_001744237.1	n.27+2421C>T		intron_variant, non_coding_transcript_variant
LOC107986620	XR_001744236.1	n.73+7758G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17142 AN: 151878 Hom.: 1018 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0902

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0778

Gnomad SAS AF: 0.0630

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.113 AC: 17149 AN: 151996 Hom.: 1020 Cov.: 33 AF XY: 0.114 AC XY: 8472 AN XY: 74274

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0904

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0778

Gnomad4 SAS AF: 0.0631

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.106

Alfa AF: 0.115 Hom.: 177

Bravo AF: 0.108

Asia WGS AF: 0.0830 AC: 287 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.1
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484978; hg19: chr6-85070397;