rs56103849

Positions:

• chr5-68486729-T-A

Variant summary

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

The XR_948411.3(LOC105379012):​n.302+2991T>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 0.596 in 151,844 control chromosomes in the GnomAD database, including 27,506 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 0.60 (27506 hom., cov: 31)
• Consequence: LOC105379012 XR_948411.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

Genes affected

LOC105379013 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379013	XR_007058804.1	n.474-53144A>T		intron_variant, non_coding_transcript_variant
LOC105379012	XR_948411.3	n.302+2991T>A		intron_variant, non_coding_transcript_variant
LOC105379013	XR_007058805.1	n.144-53144A>T		intron_variant, non_coding_transcript_variant
LOC105379013	XR_007058806.1	n.2260-53144A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90452 AN: 151726 Hom.: 27484 Cov.: 31

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.596 AC: 90504 AN: 151844 Hom.: 27506 Cov.: 31 AF XY: 0.593 AC XY: 44001 AN XY: 74222

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.570

Alfa AF: 0.610 Hom.: 3508

Bravo AF: 0.582

Asia WGS AF: 0.419 AC: 1462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56103849; hg19: chr5-67782556; COSMIC: COSV60151346;