rs1013697

Variant names:

• chr7-52421501-G-A
• rs1013697
• XR_007060636.1:n.456-3648G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-52421501-G-A
• chr7-52421501-G-C
• chr7-52421501-G-T

Variant summary

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

The XR_007060636.1(LOC124901810):​n.456-3648G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.987 in 152,266 control chromosomes in the GnomAD database, including 74,268 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 0.99 (74268 hom., cov: 31)
• Consequence: LOC124901810 XR_007060636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 1 publications found

Genes affected

LOC124901810 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 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: 0.987 AC: 150233 AN: 152148 Hom.: 74215 Cov.: 31

Gnomad AFR AF: 0.998

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.992

Gnomad FIN AF: 0.986

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.988

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

GnomAD4 genome AF: 0.987 AC: 150343 AN: 152266 Hom.: 74268 Cov.: 31 AF XY: 0.986 AC XY: 73412 AN XY: 74446

African (AFR) AF: 0.998 AC: 41458 AN: 41556

American (AMR) AF: 0.936 AC: 14298 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3415 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5152 AN: 5162

South Asian (SAS) AF: 0.992 AC: 4782 AN: 4822

European-Finnish (FIN) AF: 0.986 AC: 10465 AN: 10612

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67478 AN: 68038

Other (OTH) AF: 0.988 AC: 2091 AN: 2116

Alfa AF: 0.988 Hom.: 15080

Bravo AF: 0.983

Asia WGS AF: 0.991 AC: 3448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.020
DANN	Benign	0.41
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1013697; hg19: chr7-52489197;