rs6806731

chr3-104416411-G-A

Variant summary

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

The XR_924301.3(LOC105374020):n.165+40099C>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 0.717 in 152,022 control chromosomes in the GnomAD database, including 39,635 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 0.72 (39635 hom., cov: 31)
• Consequence: LOC105374020 XR_924301.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836

Genes affected

LOC105374020 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374020	XR_924301.3	n.165+40099C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108977 AN: 151904 Hom.: 39607 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.717 AC: 109045 AN: 152022 Hom.: 39635 Cov.: 31 AF XY: 0.720 AC XY: 53480 AN XY: 74306

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.708

Alfa AF: 0.746 Hom.: 82680

Bravo AF: 0.706

Asia WGS AF: 0.728 AC: 2520 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.055
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6806731; hg19: chr3-104135255; COSMIC: COSV56464222;