chr6-160701189-C-T

Variant names:

• chr6-160701189-C-T
• rs4252052
• ENST00000448126.6:n.985C>T

Variant summary

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

The ENST00000448126.6(ENSG00000224477):​n.985C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,114 control chromosomes in the GnomAD database, including 1,112 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 0.11 (1112 hom., cov: 32)
• Consequence: ENSG00000224477 ENST00000448126.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 3 publications found

Genes affected

ENSG00000224477 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224477	ENST00000448126.6	n.985C>T		non_coding_transcript_exon_variant	Exon 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16649 AN: 151996 Hom.: 1109 Cov.: 32

Gnomad AFR AF: 0.0304

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.0945

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

GnomAD4 genome AF: 0.110 AC: 16659 AN: 152114 Hom.: 1112 Cov.: 32 AF XY: 0.107 AC XY: 7973 AN XY: 74378

African (AFR) AF: 0.0303 AC: 1259 AN: 41548

American (AMR) AF: 0.113 AC: 1723 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3468

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5184

South Asian (SAS) AF: 0.127 AC: 611 AN: 4814

European-Finnish (FIN) AF: 0.116 AC: 1229 AN: 10578

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10912 AN: 67930

Other (OTH) AF: 0.0935 AC: 197 AN: 2106

Alfa AF: 0.128 Hom.: 183

Bravo AF: 0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.023
DANN	Benign	0.54
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4252052; hg19: chr6-161122221;