7-108826397-A-T

Variant names:

• chr7-108826397-A-T
• rs1568855
• XR_001745322.1:n.378-14260A>T

Variant summary

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

The XR_001745322.1(LOC107986836):​n.378-14260A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 152,202 control chromosomes in the GnomAD database, including 62,375 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 0.90 (62375 hom., cov: 33)
• Consequence: LOC107986836 XR_001745322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 1 publications found

Genes affected

LOC107986836 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986836	XR_001745322.1	n.378-14260A>T		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.901 AC: 137094 AN: 152084 Hom.: 62346 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.901 AC: 137176 AN: 152202 Hom.: 62375 Cov.: 33 AF XY: 0.901 AC XY: 67059 AN XY: 74420

African (AFR) AF: 0.767 AC: 31820 AN: 41502

American (AMR) AF: 0.951 AC: 14534 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3208 AN: 3472

East Asian (EAS) AF: 0.938 AC: 4848 AN: 5170

South Asian (SAS) AF: 0.955 AC: 4607 AN: 4822

European-Finnish (FIN) AF: 0.927 AC: 9838 AN: 10612

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.959 AC: 65245 AN: 68024

Other (OTH) AF: 0.909 AC: 1919 AN: 2112

Alfa AF: 0.929 Hom.: 8201

Bravo AF: 0.896

Asia WGS AF: 0.931 AC: 3235 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.49
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1568855; hg19: chr7-108466841;