chr6-160698207-C-T

Variant names:

• chr6-160698207-C-T
• rs783144
• ENST00000448126.6:n.56C>T

Variant summary

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

The ENST00000448126.6(ENSG00000224477):​n.56C>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 0.263 in 152,136 control chromosomes in the GnomAD database, including 6,328 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 0.26 (6327 hom., cov: 31)
  • Exomes 𝑓: 0.22 (1 hom.)
• Consequence: ENSG00000224477 ENST00000448126.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 13 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448126.6. 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
	ENSG00000224477	ENST00000448126.6	TSL:5	n.56C>T		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40044 AN: 151986 Hom.: 6329 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.275

GnomAD4 exome AF: 0.219 AC: 7 AN: 32 Hom.: 1 AF XY: 0.192 AC XY: 5 AN XY: 26

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.233 AC: 7 AN: 30

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.263 AC: 40049 AN: 152104 Hom.: 6327 Cov.: 31 AF XY: 0.270 AC XY: 20103 AN XY: 74338

African (AFR) AF: 0.124 AC: 5162 AN: 41506

American (AMR) AF: 0.410 AC: 6262 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 907 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3277 AN: 5174

South Asian (SAS) AF: 0.364 AC: 1749 AN: 4810

European-Finnish (FIN) AF: 0.261 AC: 2762 AN: 10566

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19056 AN: 67978

Other (OTH) AF: 0.272 AC: 576 AN: 2116

Alfa AF: 0.166 Hom.: 373

Bravo AF: 0.270

Asia WGS AF: 0.447 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.82
PhyloP100		-0.082

Splicing

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

Other links and lift over

dbSNP: rs783144; hg19: chr6-161119239; COSMIC: COSV51981736;