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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901810	XR_007060636.1	n.456-3648G>A		intron_variant	Intron 2 of 3
LOC124901810	XR_007060637.1	n.572-3648G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;