rs2030974

Positions:

• chr7-130266043-T-C

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 0.301 in 152,112 control chromosomes in the GnomAD database, including 7,341 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 0.30 (7341 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 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: 0.301 AC: 45817 AN: 151994 Hom.: 7335 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.301 AC: 45848 AN: 152112 Hom.: 7341 Cov.: 33 AF XY: 0.295 AC XY: 21939 AN XY: 74382

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.301

Alfa AF: 0.303 Hom.: 8804

Bravo AF: 0.306

Asia WGS AF: 0.146 AC: 507 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.10
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2030974; hg19: chr7-129905883;