7-108819472-C-T

Position:

• chr7-108819472-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745322.1(LOC107986836):​n.378-21185C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,066 control chromosomes in the GnomAD database, including 52,707 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 0.80 (52707 hom., cov: 31)
• Consequence: LOC107986836 XR_001745322.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

Genes affected

LOC107986836 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986836	XR_001745322.1	n.378-21185C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121082 AN: 151948 Hom.: 52700 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.796 AC: 121105 AN: 152066 Hom.: 52707 Cov.: 31 AF XY: 0.801 AC XY: 59507 AN XY: 74334

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.907

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.955

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.957

Gnomad4 OTH AF: 0.836

Alfa AF: 0.864 Hom.: 7441

Bravo AF: 0.775

Asia WGS AF: 0.898 AC: 3123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1525200; hg19: chr7-108459916;