7-23898387-C-T

Position:

• chr7-23898387-C-T

Variant summary

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

The variant allele was found at a frequency of 0.593 in 151,480 control chromosomes in the GnomAD database, including 27,959 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 0.59 (27959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.593 AC: 89718 AN: 151358 Hom.: 27914 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.593 AC: 89822 AN: 151480 Hom.: 27959 Cov.: 32 AF XY: 0.591 AC XY: 43677 AN XY: 73926

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.539

Alfa AF: 0.537 Hom.: 2692

Bravo AF: 0.613

Asia WGS AF: 0.671 AC: 2324 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1074548; hg19: chr7-23938006; COSMIC: COSV69829541;