7-25340079-T-C

Position:

• chr7-25340079-T-C

Variant summary

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

The XR_927105.2(LOC105375195):​n.890+8614T>C 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 0.515 in 152,018 control chromosomes in the GnomAD database, including 20,228 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 0.51 (20228 hom., cov: 32)
• Consequence: LOC105375195 XR_927105.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

LOC105375195 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375195	XR_927105.2	n.890+8614T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78191 AN: 151900 Hom.: 20210 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.515 AC: 78266 AN: 152018 Hom.: 20228 Cov.: 32 AF XY: 0.514 AC XY: 38198 AN XY: 74300

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.543

Alfa AF: 0.442 Hom.: 2447

Bravo AF: 0.523

Asia WGS AF: 0.497 AC: 1729 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs994531; hg19: chr7-25379698; COSMIC: COSV53495416;