rs7810486

Variant names:

• chr7-143310018-G-A
• rs7810486

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 0.396 in 152,050 control chromosomes in the GnomAD database, including 14,521 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 0.40 (14521 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 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: 0.396 AC: 60131 AN: 151932 Hom.: 14478 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.396 AC: 60221 AN: 152050 Hom.: 14521 Cov.: 32 AF XY: 0.385 AC XY: 28590 AN XY: 74336

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.0440

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.411

Alfa AF: 0.337 Hom.: 4465

Bravo AF: 0.415

Asia WGS AF: 0.222 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.71
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7810486; hg19: chr7-143007111;