7-150342466-C-T

Position:

• chr7-150342466-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647589.1(ENSG00000261305):​n.413C>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 0.219 in 133,858 control chromosomes in the GnomAD database, including 3,611 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 0.22 (3609 hom., cov: 31)
  • Exomes 𝑓: 0.36 (2 hom.)
• Consequence: ENSG00000261305 ENST00000647589.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

Genes affected

ENSG00000261305 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986858	XR_001745420.3	n.493+129C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000261305	ENST00000563946.1	n.696C>T		non_coding_transcript_exon_variant	1/1	6
ENSG00000261305	ENST00000647589.1	n.413C>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 29285 AN: 133788 Hom.: 3616 Cov.: 31

Gnomad AFR AF: 0.0775

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.212

GnomAD4 exome AF: 0.364 AC: 8 AN: 22 Hom.: 2 Cov.: 0 AF XY: 0.357 AC XY: 5 AN XY: 14

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.219 AC: 29266 AN: 133836 Hom.: 3609 Cov.: 31 AF XY: 0.220 AC XY: 14467 AN XY: 65790

Gnomad4 AFR AF: 0.0775

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.209

Alfa AF: 0.238 Hom.: 2740

Bravo AF: 0.176

Asia WGS AF: 0.259 AC: 897 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3735167; hg19: chr7-150039555;