7-12210267-C-T

Variant names:

• chr7-12210267-C-T
• rs1435528
• ENST00000757744.1:n.906G>A

Variant summary

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

The ENST00000757744.1(ENSG00000298754):​n.906G>A 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 0.761 in 152,150 control chromosomes in the GnomAD database, including 44,916 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 0.76 (44916 hom., cov: 32)
• Consequence: ENSG00000298754 ENST00000757744.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58
• Publications: 6 publications found

Genes affected

ENSG00000298754 (HGNC:):

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 = 0.929 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757744.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298754	ENST00000757744.1		n.906G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115611 AN: 152030 Hom.: 44862 Cov.: 32

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.761 AC: 115720 AN: 152150 Hom.: 44916 Cov.: 32 AF XY: 0.760 AC XY: 56521 AN XY: 74370

African (AFR) AF: 0.937 AC: 38947 AN: 41558

American (AMR) AF: 0.738 AC: 11280 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2461 AN: 3472

East Asian (EAS) AF: 0.680 AC: 3508 AN: 5160

South Asian (SAS) AF: 0.728 AC: 3513 AN: 4824

European-Finnish (FIN) AF: 0.695 AC: 7344 AN: 10572

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.681 AC: 46311 AN: 67968

Other (OTH) AF: 0.736 AC: 1555 AN: 2112

Alfa AF: 0.705 Hom.: 63982

Bravo AF: 0.771

Asia WGS AF: 0.727 AC: 2526 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.093
DANN	Benign	0.63
PhyloP100		-3.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1435528;

hg19: chr7-12249893;