7-77010554-T-C

Position:

• chr7-77010554-T-C

Variant summary

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

The NR_023383.1(DTX2P1-UPK3BP1-PMS2P11):​n.1096-1326T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.83 (46664 hom., cov: 16)
• Consequence: DTX2P1-UPK3BP1-PMS2P11 NR_023383.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

Genes affected

DTX2P1-UPK3BP1-PMS2P11 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DTX2P1-UPK3BP1-PMS2P11	NR_023383.1	n.1096-1326T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.831 AC: 110031 AN: 132458 Hom.: 46614 Cov.: 16

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.773

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.831 AC: 110123 AN: 132556 Hom.: 46664 Cov.: 16 AF XY: 0.818 AC XY: 51883 AN XY: 63450

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.802

Alfa AF: 0.842 Hom.: 17193

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6955651; hg19: chr7-76639871; COSMIC: COSV50831096;