6-163978346-C-T

Position:

• chr6-163978346-C-T

Variant summary

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

The ENST00000659063.1(ENSG00000288696):​n.43-30178C>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 0.261 in 152,094 control chromosomes in the GnomAD database, including 5,441 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 0.26 (5441 hom., cov: 32)
• Consequence: ENST00000659063.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378102	XR_943213.4	n.558+58432C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659063.1	n.43-30178C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39645 AN: 151976 Hom.: 5431 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.261 AC: 39687 AN: 152094 Hom.: 5441 Cov.: 32 AF XY: 0.256 AC XY: 19070 AN XY: 74360

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.256

Alfa AF: 0.249 Hom.: 605

Bravo AF: 0.276

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484513; hg19: chr6-164399378;