ENST00000769333.1:n.655T>G

Variant names:

• chr7-125933854-T-G
• rs10256927
• ENST00000769333.1:n.655T>G

Variant summary

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

The ENST00000769333.1(ENSG00000197462):​n.655T>G 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 0.744 in 151,878 control chromosomes in the GnomAD database, including 42,172 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 0.74 (42171 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENSG00000197462 ENST00000769333.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 5 publications found

Genes affected

ENSG00000197462 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.806 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
ENSG00000197462	ENST00000769333.1	n.655T>G		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000197462	ENST00000769334.1	n.525T>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000197462	ENST00000769323.1	n.389+9467T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112911 AN: 151758 Hom.: 42146 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.766

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.744 AC: 112980 AN: 151876 Hom.: 42171 Cov.: 32 AF XY: 0.743 AC XY: 55131 AN XY: 74236

African (AFR) AF: 0.696 AC: 28814 AN: 41410

American (AMR) AF: 0.818 AC: 12451 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2888 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3822 AN: 5132

South Asian (SAS) AF: 0.789 AC: 3796 AN: 4814

European-Finnish (FIN) AF: 0.711 AC: 7525 AN: 10588

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51222 AN: 67926

Other (OTH) AF: 0.764 AC: 1610 AN: 2106

Alfa AF: 0.756 Hom.: 29280

Bravo AF: 0.750

Asia WGS AF: 0.747 AC: 2598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.71
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10256927; hg19: chr7-125573908;