7-95397441-T-C

Position:

• chr7-95397441-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000702974.1(ENSG00000290101):​n.945T>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 0.29 in 151,534 control chromosomes in the GnomAD database, including 6,805 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 0.29 (6805 hom., cov: 30)
• Consequence: ENSG00000290101 ENST00000702974.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

Genes affected

ENSG00000290101 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986822	XR_001745283.2	n.557+413T>C		intron_variant
LOC107986822	XR_007060439.1	n.557+413T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290101	ENST00000702974.1	n.945T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43941 AN: 151416 Hom.: 6790 Cov.: 30

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.290 AC: 43979 AN: 151534 Hom.: 6805 Cov.: 30 AF XY: 0.298 AC XY: 22088 AN XY: 74034

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.259

Alfa AF: 0.290 Hom.: 788

Bravo AF: 0.269

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11767787; hg19: chr7-95026753;