rs7798431

Variant names:

• chr7-25821192-G-A
• rs7798431

Your query was ambiguous. Multiple possible variants found:

• chr7-25821192-G-A
• chr7-25821192-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.245 in 152,050 control chromosomes in the GnomAD database, including 4,855 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 0.25 (4855 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 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: 0.245 AC: 37269 AN: 151932 Hom.: 4853 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.245 AC: 37305 AN: 152050 Hom.: 4855 Cov.: 32 AF XY: 0.253 AC XY: 18788 AN XY: 74346

Gnomad4 AFR AF: 0.195 AC: 0.195385 AN: 0.195385

Gnomad4 AMR AF: 0.215 AC: 0.214622 AN: 0.214622

Gnomad4 ASJ AF: 0.216 AC: 0.216138 AN: 0.216138

Gnomad4 EAS AF: 0.441 AC: 0.441051 AN: 0.441051

Gnomad4 SAS AF: 0.475 AC: 0.475291 AN: 0.475291

Gnomad4 FIN AF: 0.292 AC: 0.291596 AN: 0.291596

Gnomad4 NFE AF: 0.247 AC: 0.246594 AN: 0.246594

Gnomad4 OTH AF: 0.252 AC: 0.252137 AN: 0.252137

Alfa AF: 0.228 Hom.: 2731

Bravo AF: 0.233

Asia WGS AF: 0.415 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7798431; hg19: chr7-25860812;