rs508145

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000288696 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659063.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288696	ENST00000659063.1		n.42+39408T>C		intron	N/A
	ENSG00000288696	ENST00000850151.1		n.105+39525T>C		intron	N/A
	ENSG00000288696	ENST00000850152.1		n.165+39525T>C		intron	N/A

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

African (AFR) AF: 0.148 AC: 6150 AN: 41544

American (AMR) AF: 0.0403 AC: 616 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0582 AC: 202 AN: 3470

East Asian (EAS) AF: 0.0179 AC: 93 AN: 5188

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4824

European-Finnish (FIN) AF: 0.00565 AC: 60 AN: 10626

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0283 AC: 1925 AN: 68032

Other (OTH) AF: 0.0577 AC: 122 AN: 2114

Alfa AF: 0.0409 Hom.: 459

Bravo AF: 0.0670

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs508145; hg19: chr6-164387603;