7-23297888-G-C

Variant names:

• chr7-23297888-G-C
• rs199657

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 0.618 in 152,044 control chromosomes in the GnomAD database, including 29,263 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 0.62 (29263 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• 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: 0.618 AC: 93880 AN: 151926 Hom.: 29219 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.618 AC: 93974 AN: 152044 Hom.: 29263 Cov.: 32 AF XY: 0.622 AC XY: 46243 AN XY: 74320

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.597

Alfa AF: 0.599 Hom.: 3445

Bravo AF: 0.625

Asia WGS AF: 0.707 AC: 2459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.065
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs199657; hg19: chr7-23337507;