7-130735197-T-C

Variant names:

• chr7-130735197-T-C
• rs290805
• XR_001744984.2:n.119+815T>C

Variant summary

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

The XR_927976.3(LOC105375508):​n.119+815T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,180 control chromosomes in the GnomAD database, including 47,971 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 0.79 (47971 hom., cov: 32)
• Consequence: LOC105375508 XR_927976.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 1 publications found

Genes affected

LOC105375508 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120621 AN: 152062 Hom.: 47925 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.793 AC: 120725 AN: 152180 Hom.: 47971 Cov.: 32 AF XY: 0.792 AC XY: 58952 AN XY: 74414

African (AFR) AF: 0.796 AC: 33045 AN: 41494

American (AMR) AF: 0.799 AC: 12227 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2677 AN: 3468

East Asian (EAS) AF: 0.757 AC: 3922 AN: 5182

South Asian (SAS) AF: 0.793 AC: 3828 AN: 4828

European-Finnish (FIN) AF: 0.792 AC: 8388 AN: 10596

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53983 AN: 67990

Other (OTH) AF: 0.792 AC: 1676 AN: 2116

Alfa AF: 0.781 Hom.: 7275

Bravo AF: 0.792

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.4
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs290805; hg19: chr7-130419958;