7-91286039-G-A

Variant names:

• chr7-91286039-G-A
• rs2888830
• XR_007060425.1:n.126+1268C>T

Variant summary

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

The XR_007060425.1(LOC124901695):​n.126+1268C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,048 control chromosomes in the GnomAD database, including 31,754 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 0.64 (31754 hom., cov: 32)
• Consequence: LOC124901695 XR_007060425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 6 publications found

Genes affected

LOC124901695 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.672 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: 0.645 AC: 97961 AN: 151930 Hom.: 31744 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.645 AC: 97998 AN: 152048 Hom.: 31754 Cov.: 32 AF XY: 0.643 AC XY: 47806 AN XY: 74306

African (AFR) AF: 0.586 AC: 24279 AN: 41442

American (AMR) AF: 0.683 AC: 10439 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2178 AN: 3472

East Asian (EAS) AF: 0.639 AC: 3305 AN: 5172

South Asian (SAS) AF: 0.630 AC: 3029 AN: 4810

European-Finnish (FIN) AF: 0.632 AC: 6664 AN: 10540

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45839 AN: 68000

Other (OTH) AF: 0.644 AC: 1362 AN: 2116

Alfa AF: 0.667 Hom.: 92818

Bravo AF: 0.649

Asia WGS AF: 0.559 AC: 1945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.78
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs2888830; hg19: chr7-90915354;