6-149977706-C-T

Variant names:

• chr6-149977706-C-T
• rs1853665
• ENST00000406262.1:n.236C>T

Variant summary

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

The ENST00000406262.1(ENSG00000219298):​n.236C>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 0.202 in 850,378 control chromosomes in the GnomAD database, including 21,083 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 0.27 (6700 hom., cov: 33)
  • Exomes 𝑓: 0.19 (14383 hom.)
• Consequence: ENSG00000219298 ENST00000406262.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 27 publications found

Genes affected

ENSG00000219298 (HGNC:):

BTF3P10 (HGNC:38570): (basic transcription factor 3 pseudogene 10)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 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
ENSG00000219298	ENST00000406262.1	n.236C>T		non_coding_transcript_exon_variant	Exon 1 of 2	6
BTF3P10	ENST00000433415.1	n.-216C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40320 AN: 151994 Hom.: 6675 Cov.: 33

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.259

GnomAD4 exome AF: 0.189 AC: 131808 AN: 698266 Hom.: 14383 Cov.: 9 AF XY: 0.186 AC XY: 69095 AN XY: 372204

African (AFR) AF: 0.455 AC: 8465 AN: 18610

American (AMR) AF: 0.260 AC: 10625 AN: 40836

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 4420 AN: 19220

East Asian (EAS) AF: 0.376 AC: 11525 AN: 30660

South Asian (SAS) AF: 0.179 AC: 12775 AN: 71388

European-Finnish (FIN) AF: 0.177 AC: 7882 AN: 44580

Middle Eastern (MID) AF: 0.276 AC: 1128 AN: 4084

European-Non Finnish (NFE) AF: 0.156 AC: 68108 AN: 436004

Other (OTH) AF: 0.209 AC: 6880 AN: 32884

GnomAD4 genome AF: 0.265 AC: 40385 AN: 152112 Hom.: 6700 Cov.: 33 AF XY: 0.266 AC XY: 19811 AN XY: 74356

African (AFR) AF: 0.453 AC: 18786 AN: 41456

American (AMR) AF: 0.285 AC: 4350 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3468

East Asian (EAS) AF: 0.365 AC: 1887 AN: 5172

South Asian (SAS) AF: 0.181 AC: 872 AN: 4824

European-Finnish (FIN) AF: 0.192 AC: 2033 AN: 10584

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10899 AN: 68002

Other (OTH) AF: 0.256 AC: 542 AN: 2114

Alfa AF: 0.194 Hom.: 15094

Bravo AF: 0.280

Asia WGS AF: 0.270 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.51
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1853665; hg19: chr6-150298842; COSMIC: COSV57663437;