6-163972212-G-T

Variant names:

• chr6-163972212-G-T
• rs10428875
• ENST00000659063.1:n.43-36312G>T

Variant summary

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

The ENST00000659063.1(ENSG00000288696):​n.43-36312G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,064 control chromosomes in the GnomAD database, including 6,856 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 0.29 (6856 hom., cov: 33)
• Consequence: ENSG00000288696 ENST00000659063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759

Genes affected

ENSG00000288696 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378102	XR_943213.4	n.558+52298G>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288696	ENST00000659063.1	n.43-36312G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43405 AN: 151946 Hom.: 6838 Cov.: 33

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.286 AC: 43463 AN: 152064 Hom.: 6856 Cov.: 33 AF XY: 0.282 AC XY: 20960 AN XY: 74360

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.277

Alfa AF: 0.258 Hom.: 1279

Bravo AF: 0.304

Asia WGS AF: 0.205 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0070
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10428875; hg19: chr6-164393244;