chr7-25952206-T-C

Variant names:

• chr7-25952206-T-C
• rs4722551
• ENST00000689370.3:n.773T>C

Variant summary

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

The ENST00000689370.3(ENSG00000288962):​n.773T>C 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 0.131 in 152,144 control chromosomes in the GnomAD database, including 1,655 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 0.13 (1655 hom., cov: 32)
• Consequence: ENSG00000288962 ENST00000689370.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 73 publications found

Genes affected

ENSG00000288962 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375199	XR_927114.3	n.1314-12745A>G		intron_variant	Intron 6 of 6
LOC105375199	XR_927122.3	n.541-12745A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288962	ENST00000689370.3	n.773T>C		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000293754	ENST00000718758.1	n.605-12745A>G		intron_variant	Intron 3 of 3
ENSG00000293754	ENST00000718759.1	n.682-52A>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19863 AN: 152026 Hom.: 1651 Cov.: 32

Gnomad AFR AF: 0.0471

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0233

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.131 AC: 19881 AN: 152144 Hom.: 1655 Cov.: 32 AF XY: 0.133 AC XY: 9917 AN XY: 74364

African (AFR) AF: 0.0471 AC: 1957 AN: 41534

American (AMR) AF: 0.173 AC: 2644 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3470

East Asian (EAS) AF: 0.0233 AC: 121 AN: 5188

South Asian (SAS) AF: 0.114 AC: 551 AN: 4816

European-Finnish (FIN) AF: 0.236 AC: 2489 AN: 10552

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11206 AN: 67980

Other (OTH) AF: 0.119 AC: 252 AN: 2110

Alfa AF: 0.145 Hom.: 6924

Bravo AF: 0.120

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.90
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs4722551; hg19: chr7-25991826;