XR_007062691.1:n.1397+2072C>G

Variant names:

• chr11-61185242-C-G
• rs612386
• XR_007062691.1:n.1397+2072C>G

Variant summary

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

The XR_007062691.1(LOC124902678):​n.1397+2072C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 151,618 control chromosomes in the GnomAD database, including 35,229 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 0.67 (35229 hom., cov: 31)
• Consequence: LOC124902678 XR_007062691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 2 publications found

Genes affected

LOC124902678 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.665 AC: 100731 AN: 151502 Hom.: 35173 Cov.: 31

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.665 AC: 100845 AN: 151618 Hom.: 35229 Cov.: 31 AF XY: 0.672 AC XY: 49785 AN XY: 74082

African (AFR) AF: 0.820 AC: 33700 AN: 41092

American (AMR) AF: 0.683 AC: 10411 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1871 AN: 3468

East Asian (EAS) AF: 0.997 AC: 5165 AN: 5182

South Asian (SAS) AF: 0.844 AC: 4054 AN: 4806

European-Finnish (FIN) AF: 0.647 AC: 6837 AN: 10566

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36840 AN: 67958

Other (OTH) AF: 0.629 AC: 1323 AN: 2102

Alfa AF: 0.595 Hom.: 3341

Bravo AF: 0.672

Asia WGS AF: 0.914 AC: 3179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.47
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs612386; hg19: chr11-60952714;