rs7004029

Variant names:

• chr8-144720652-T-C
• rs7004029

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 0.36 in 152,140 control chromosomes in the GnomAD database, including 10,822 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 0.36 (10822 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.562 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: 0.360 AC: 54780 AN: 152022 Hom.: 10827 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.360 AC: 54783 AN: 152140 Hom.: 10822 Cov.: 33 AF XY: 0.368 AC XY: 27340 AN XY: 74372

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.368

Alfa AF: 0.402 Hom.: 6123

Bravo AF: 0.340

Asia WGS AF: 0.541 AC: 1880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7004029; hg19: chr8-145946037;