2-75612607-T-C

Variant names:

• chr2-75612607-T-C
• rs6732511
• XR_007087115.1:n.679-1244T>C

Variant summary

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

The XR_007087115.1(LOC124906026):​n.679-1244T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 152,176 control chromosomes in the GnomAD database, including 59,919 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 0.89 (59919 hom., cov: 30)
• Consequence: LOC124906026 XR_007087115.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315
• Publications: 9 publications found

Genes affected

LOC124906026 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.95 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: 0.886 AC: 134689 AN: 152058 Hom.: 59868 Cov.: 30

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.886 AC: 134796 AN: 152176 Hom.: 59919 Cov.: 30 AF XY: 0.887 AC XY: 65959 AN XY: 74374

African (AFR) AF: 0.958 AC: 39777 AN: 41536

American (AMR) AF: 0.904 AC: 13836 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2866 AN: 3472

East Asian (EAS) AF: 0.947 AC: 4893 AN: 5166

South Asian (SAS) AF: 0.878 AC: 4236 AN: 4822

European-Finnish (FIN) AF: 0.852 AC: 9000 AN: 10566

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57276 AN: 68008

Other (OTH) AF: 0.880 AC: 1853 AN: 2106

Alfa AF: 0.856 Hom.: 247625

Bravo AF: 0.891

Asia WGS AF: 0.924 AC: 3215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.6
DANN	Benign	0.76
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs6732511; hg19: chr2-75839733;