rs6796709

Positions:

• chr3-118791784-G-A

Variant summary

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

The NR_135547.1(LOC105374060):​n.127+18923C>T 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 0.0188 in 152,212 control chromosomes in the GnomAD database, including 95 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 0.019 (95 hom., cov: 32)
• Consequence: LOC105374060 NR_135547.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.890

Genes affected

LOC105374060 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.095 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374060	NR_135547.1	n.127+18923C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656350.1	n.130+18923C>T		intron_variant, non_coding_transcript_variant
	ENST00000657445.1	n.51+18923C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0187 AC: 2847 AN: 152094 Hom.: 90 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0387

Gnomad FIN AF: 0.00274

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00784

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0188 AC: 2867 AN: 152212 Hom.: 95 Cov.: 32 AF XY: 0.0209 AC XY: 1555 AN XY: 74416

Gnomad4 AFR AF: 0.0110

Gnomad4 AMR AF: 0.0654

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0390

Gnomad4 FIN AF: 0.00274

Gnomad4 NFE AF: 0.00784

Gnomad4 OTH AF: 0.0236

Alfa AF: 0.0129 Hom.: 9

Bravo AF: 0.0239

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6796709; hg19: chr3-118510631;