chr7-87913722-C-G

Variant names:

• chr7-87913722-C-G
• rs6966264
• XR_007060414.1:n.434G>C

Variant summary

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

The XR_007060414.1(LOC124901690):​n.434G>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 0.0318 in 152,300 control chromosomes in the GnomAD database, including 131 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 0.032 (131 hom., cov: 32)
• Consequence: LOC124901690 XR_007060414.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 1 publications found

Genes affected

LOC124901690 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0738 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: 0.0317 AC: 4817 AN: 152182 Hom.: 128 Cov.: 32

Gnomad AFR AF: 0.0758

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0111

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.0392

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0133

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0318 AC: 4837 AN: 152300 Hom.: 131 Cov.: 32 AF XY: 0.0319 AC XY: 2375 AN XY: 74474

African (AFR) AF: 0.0760 AC: 3158 AN: 41564

American (AMR) AF: 0.0110 AC: 169 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 72 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0135 AC: 65 AN: 4832

European-Finnish (FIN) AF: 0.0392 AC: 416 AN: 10604

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0133 AC: 904 AN: 68026

Other (OTH) AF: 0.0232 AC: 49 AN: 2114

Alfa AF: 0.0241 Hom.: 6

Bravo AF: 0.0317

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.3
DANN	Benign	0.90
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs6966264; hg19: chr7-87543037;