chr6-163972212-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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.43-36312G>T		intron	N/A
	ENSG00000288696	ENST00000850151.1		n.105+45166G>T		intron	N/A
	ENSG00000288696	ENST00000850152.1		n.165+45166G>T		intron	N/A

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

African (AFR) AF: 0.427 AC: 17723 AN: 41458

American (AMR) AF: 0.304 AC: 4650 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1235 AN: 5142

South Asian (SAS) AF: 0.166 AC: 801 AN: 4822

European-Finnish (FIN) AF: 0.186 AC: 1974 AN: 10610

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15693 AN: 67960

Other (OTH) AF: 0.277 AC: 585 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0070
DANN	Benign	0.54
PhyloP100		-0.76

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10428875;

hg19: chr6-164393244;