chr6-142628172-G-T

Variant names:

• chr6-142628172-G-T
• rs263153
• ENST00000447311.1:n.177+9541C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000447311.1(ENSG00000236366):​n.177+9541C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0991 in 152,158 control chromosomes in the GnomAD database, including 851 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 0.099 (851 hom., cov: 32)
• Consequence: ENSG00000236366 ENST00000447311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 0 publications found

Genes affected

ENSG00000236366 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447311.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC153910	NR_027311.1		n.124+9541C>A		intron	N/A
	LOC153910	NR_027312.1		n.177+9541C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236366	ENST00000447311.1	TSL:2	n.177+9541C>A		intron	N/A
	ENSG00000236366	ENST00000635073.1	TSL:4	n.63+9541C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0991 AC: 15061 AN: 152040 Hom.: 852 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0673

Gnomad ASJ AF: 0.0929

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0279

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0920

Gnomad OTH AF: 0.0864

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

GnomAD4 genome AF: 0.0991 AC: 15072 AN: 152158 Hom.: 851 Cov.: 32 AF XY: 0.0994 AC XY: 7398 AN XY: 74390

African (AFR) AF: 0.138 AC: 5712 AN: 41504

American (AMR) AF: 0.0672 AC: 1027 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0929 AC: 322 AN: 3466

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0281 AC: 136 AN: 4834

European-Finnish (FIN) AF: 0.127 AC: 1344 AN: 10584

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0920 AC: 6252 AN: 67992

Other (OTH) AF: 0.0846 AC: 179 AN: 2116

Alfa AF: 0.0907 Hom.: 381

Bravo AF: 0.0954

Asia WGS AF: 0.0270 AC: 95 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.053
DANN	Benign	0.50
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs263153; hg19: chr6-142949309;