chr7-23898387-C-T

Variant names:

• chr7-23898387-C-T
• rs1074548

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;