7-130748625-C-T

Variant names:

• chr7-130748625-C-T
• rs4731702
• XR_007060527.1:n.178+10635C>T

Variant summary

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

The XR_927976.3(LOC105375508):​n.178+10635C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,010 control chromosomes in the GnomAD database, including 13,021 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 0.40 (13021 hom., cov: 32)
• Consequence: LOC105375508 XR_927976.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 119 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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: 0.401 AC: 60954 AN: 151892 Hom.: 13015 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.401 AC: 60973 AN: 152010 Hom.: 13021 Cov.: 32 AF XY: 0.398 AC XY: 29548 AN XY: 74312

African (AFR) AF: 0.268 AC: 11124 AN: 41484

American (AMR) AF: 0.388 AC: 5934 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1588 AN: 5180

South Asian (SAS) AF: 0.392 AC: 1885 AN: 4814

European-Finnish (FIN) AF: 0.448 AC: 4724 AN: 10536

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33158 AN: 67932

Other (OTH) AF: 0.423 AC: 889 AN: 2104

Alfa AF: 0.454 Hom.: 53857

Bravo AF: 0.390

Asia WGS AF: 0.377 AC: 1308 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.87
DANN	Benign	0.46
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4731702; hg19: chr7-130433384;