7-25855101-T-C

Variant names:

• chr7-25855101-T-C
• rs1451385
• ENST00000812211.1:n.614A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000812211.1(ENSG00000286725):​n.614A>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 0.627 in 152,130 control chromosomes in the GnomAD database, including 31,869 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 0.63 (31869 hom., cov: 33)
• Consequence: ENSG00000286725 ENST00000812211.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.778
• Publications: 8 publications found

Genes affected

ENSG00000286725 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 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
ENSG00000286725	ENST00000812211.1	n.614A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000286725	ENST00000812216.1	n.941A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000286725	ENST00000666265.2	n.221+7043A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95426 AN: 152012 Hom.: 31877 Cov.: 33

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.656

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.627 AC: 95448 AN: 152130 Hom.: 31869 Cov.: 33 AF XY: 0.623 AC XY: 46300 AN XY: 74370

African (AFR) AF: 0.442 AC: 18330 AN: 41484

American (AMR) AF: 0.677 AC: 10340 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2710 AN: 3470

East Asian (EAS) AF: 0.180 AC: 932 AN: 5176

South Asian (SAS) AF: 0.492 AC: 2377 AN: 4828

European-Finnish (FIN) AF: 0.712 AC: 7532 AN: 10576

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50876 AN: 68004

Other (OTH) AF: 0.652 AC: 1378 AN: 2112

Alfa AF: 0.589 Hom.: 6459

Bravo AF: 0.615

Asia WGS AF: 0.406 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	19
DANN	Benign	0.64
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs1451385; hg19: chr7-25894721;