rs1343391

chr6-58017876-C-G

Variant summary

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

The ENST00000641775.1(ENSG00000225096):n.172-9796C>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 0.401 in 151,926 control chromosomes in the GnomAD database, including 13,108 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 0.40 (13108 hom., cov: 31)
• Consequence: ENST00000641775.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927293	XR_001744180.1	n.3472-9796C>G		intron_variant, non_coding_transcript_variant
LOC101927293	XR_007059624.1	n.989-9796C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641775.1	n.172-9796C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60840 AN: 151808 Hom.: 13107 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.401 AC: 60863 AN: 151926 Hom.: 13108 Cov.: 31 AF XY: 0.408 AC XY: 30317 AN XY: 74264

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.423

Alfa AF: 0.412 Hom.: 1697

Bravo AF: 0.400

Asia WGS AF: 0.461 AC: 1601 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1343391; hg19: chr6-58344154;