XR_007060445.1:n.132-7603C>G

Variant names:

• chr7-97187952-G-C
• rs6970451
• XR_007060445.1:n.132-7603C>G

Variant summary

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

The XR_007060445.1(LOC124901704):​n.132-7603C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,102 control chromosomes in the GnomAD database, including 5,727 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 0.25 (5727 hom., cov: 32)
• Consequence: LOC124901704 XR_007060445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 1 publications found

Genes affected

LOC124901704 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38317 AN: 151986 Hom.: 5731 Cov.: 32

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.252 AC: 38294 AN: 152102 Hom.: 5727 Cov.: 32 AF XY: 0.252 AC XY: 18703 AN XY: 74358

African (AFR) AF: 0.0947 AC: 3932 AN: 41522

American (AMR) AF: 0.206 AC: 3152 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3470

East Asian (EAS) AF: 0.383 AC: 1980 AN: 5172

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4816

European-Finnish (FIN) AF: 0.308 AC: 3252 AN: 10546

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22227 AN: 67972

Other (OTH) AF: 0.266 AC: 563 AN: 2114

Alfa AF: 0.190 Hom.: 455

Bravo AF: 0.239

Asia WGS AF: 0.300 AC: 1042 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.83
DANN	Benign	0.62
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6970451; hg19: chr7-96817264;