ENST00000766149.1:n.1009C>T

Variant names:

• chr7-12570053-G-A
• rs3735222
• ENST00000766149.1:n.1009C>T

Variant summary

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

The ENST00000766149.1(ENSG00000225606):​n.1009C>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 0.431 in 151,990 control chromosomes in the GnomAD database, including 14,389 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 0.43 (14388 hom., cov: 33)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ENSG00000225606 ENST00000766149.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 8 publications found

Genes affected

ENSG00000225606 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986768	XR_007060635.1	n.2175C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225606	ENST00000766149.1	n.1009C>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000225606	ENST00000766153.1	n.1602C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000225606	ENST00000766155.1	n.1366C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65432 AN: 151866 Hom.: 14370 Cov.: 33

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.425

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 AF XY: 0.500 AC XY: 3 AN XY: 6

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) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.431 AC: 65482 AN: 151984 Hom.: 14388 Cov.: 33 AF XY: 0.425 AC XY: 31566 AN XY: 74258

African (AFR) AF: 0.494 AC: 20449 AN: 41428

American (AMR) AF: 0.404 AC: 6169 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1515 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1194 AN: 5172

South Asian (SAS) AF: 0.362 AC: 1740 AN: 4812

European-Finnish (FIN) AF: 0.367 AC: 3867 AN: 10530

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.428 AC: 29062 AN: 67972

Other (OTH) AF: 0.421 AC: 888 AN: 2110

Alfa AF: 0.428 Hom.: 45646

Bravo AF: 0.434

Asia WGS AF: 0.298 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.45
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs3735222; hg19: chr7-12609679;