7-153227808-A-G

Variant names:

• chr7-153227808-A-G
• rs2710201
• XR_007060599.1:n.2089-639A>G

Variant summary

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

The XR_007060599.1(LOC102723686):​n.2089-639A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,052 control chromosomes in the GnomAD database, including 6,942 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 0.21 (6942 hom., cov: 32)
• Consequence: LOC102723686 XR_007060599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 6 publications found

Genes affected

LOC102723686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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: 0.209 AC: 31701 AN: 151934 Hom.: 6917 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.0771

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.0642

Gnomad SAS AF: 0.0875

Gnomad FIN AF: 0.0934

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.209 AC: 31774 AN: 152052 Hom.: 6942 Cov.: 32 AF XY: 0.207 AC XY: 15367 AN XY: 74354

African (AFR) AF: 0.557 AC: 23068 AN: 41408

American (AMR) AF: 0.164 AC: 2503 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 157 AN: 3470

East Asian (EAS) AF: 0.0638 AC: 330 AN: 5176

South Asian (SAS) AF: 0.0865 AC: 417 AN: 4820

European-Finnish (FIN) AF: 0.0934 AC: 990 AN: 10598

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0567 AC: 3858 AN: 67986

Other (OTH) AF: 0.170 AC: 359 AN: 2112

Alfa AF: 0.104 Hom.: 6243

Bravo AF: 0.229

Asia WGS AF: 0.121 AC: 422 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.42
DANN	Benign	0.38
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2710201; hg19: chr7-152924893;