rs7004029

Positions:

• chr8-144720652-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 0.36 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;