rs7004938

Variant names:

• chr8-139246982-G-A
• rs7004938

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 0.355 in 151,880 control chromosomes in the GnomAD database, including 10,406 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 0.35 (10406 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.12).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.454 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: 0.355 AC: 53883 AN: 151762 Hom.: 10396 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.355 AC: 53905 AN: 151880 Hom.: 10406 Cov.: 33 AF XY: 0.359 AC XY: 26663 AN XY: 74224

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.334

Alfa AF: 0.400 Hom.: 14911

Bravo AF: 0.346

Asia WGS AF: 0.277 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.17
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7004938; hg19: chr8-140259225;