rs508145

Variant names:

• chr6-163966571-T-C
• rs508145
• ENST00000659063.1:n.42+39408T>C

Variant summary

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

The ENST00000659063.1(ENSG00000288696):​n.42+39408T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0615 in 152,304 control chromosomes in the GnomAD database, including 525 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 0.062 (525 hom., cov: 33)
• Consequence: ENSG00000288696 ENST00000659063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

ENSG00000288696 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378102	XR_943213.4	n.558+46657T>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288696	ENST00000659063.1	n.42+39408T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0614 AC: 9350 AN: 152186 Hom.: 520 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0403

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.00565

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0615 AC: 9374 AN: 152304 Hom.: 525 Cov.: 33 AF XY: 0.0585 AC XY: 4355 AN XY: 74464

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0403

Gnomad4 ASJ AF: 0.0582

Gnomad4 EAS AF: 0.0179

Gnomad4 SAS AF: 0.0367

Gnomad4 FIN AF: 0.00565

Gnomad4 NFE AF: 0.0283

Gnomad4 OTH AF: 0.0577

Alfa AF: 0.0398 Hom.: 41

Bravo AF: 0.0670

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
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: rs508145; hg19: chr6-164387603;