rs1004168

chr7-48990724-C-Achr7-48990724-C-G

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 0.321 in 151,972 control chromosomes in the GnomAD database, including 7,972 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 0.32 (7972 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 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: 0.321 AC: 48708 AN: 151854 Hom.: 7972 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.321 AC: 48710 AN: 151972 Hom.: 7972 Cov.: 32 AF XY: 0.316 AC XY: 23506 AN XY: 74278

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.348

Alfa AF: 0.352 Hom.: 4456

Bravo AF: 0.324

Asia WGS AF: 0.300 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.0
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1004168; hg19: chr7-49030320;