chr7-130266043-T-C

Variant names:

• chr7-130266043-T-C
• rs2030974

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 0.301 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.379 AC: 15733 AN: 41472

American (AMR) AF: 0.236 AC: 3608 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1293 AN: 3472

East Asian (EAS) AF: 0.112 AC: 581 AN: 5186

South Asian (SAS) AF: 0.186 AC: 897 AN: 4822

European-Finnish (FIN) AF: 0.239 AC: 2525 AN: 10566

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20242 AN: 67994

Other (OTH) AF: 0.301 AC: 636 AN: 2114

Alfa AF: 0.303 Hom.: 10114

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2030974; hg19: chr7-129905883;