7-108824307-C-T

Variant names:

• chr7-108824307-C-T
• rs7781585
• XR_001745322.1:n.378-16350C>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.378-16350C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,154 control chromosomes in the GnomAD database, including 56,093 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 0.84 (56093 hom., cov: 33)
• Consequence: LOC107986836 XR_001745322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986836	XR_001745322.1	n.378-16350C>T		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127762 AN: 152036 Hom.: 56085 Cov.: 33

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.840 AC: 127806 AN: 152154 Hom.: 56093 Cov.: 33 AF XY: 0.843 AC XY: 62685 AN XY: 74392

African (AFR) AF: 0.555 AC: 23028 AN: 41472

American (AMR) AF: 0.926 AC: 14130 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3205 AN: 3468

East Asian (EAS) AF: 0.938 AC: 4846 AN: 5168

South Asian (SAS) AF: 0.955 AC: 4611 AN: 4830

European-Finnish (FIN) AF: 0.927 AC: 9836 AN: 10608

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.958 AC: 65164 AN: 68024

Other (OTH) AF: 0.868 AC: 1834 AN: 2114

Alfa AF: 0.878 Hom.: 7844

Bravo AF: 0.825

Asia WGS AF: 0.912 AC: 3166 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs7781585; hg19: chr7-108464751;