rs6878606

Positions:

• chr5-173437107-A-G

Variant summary

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

The ENST00000663262.1(ENSG00000253968):​n.243-2321A>G 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 0.42 in 152,078 control chromosomes in the GnomAD database, including 15,098 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 0.42 (15098 hom., cov: 32)
• Consequence: ENST00000663262.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377732	XR_001743001.1	n.162-6793A>G		intron_variant, non_coding_transcript_variant
LOC105377732	XR_007059057.1	n.161-6793A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663262.1	n.243-2321A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63799 AN: 151960 Hom.: 15058 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.420 AC: 63906 AN: 152078 Hom.: 15098 Cov.: 32 AF XY: 0.421 AC XY: 31300 AN XY: 74314

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.402

Alfa AF: 0.327 Hom.: 17086

Bravo AF: 0.427

Asia WGS AF: 0.353 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.075
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6878606; hg19: chr5-172864110;