rs7529671

Variant names:

• chr1-96983373-T-C
• rs7529671

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 0.108 in 152,160 control chromosomes in the GnomAD database, including 2,854 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 0.11 (2854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 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: 0.108 AC: 16345 AN: 152042 Hom.: 2847 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0360

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00356

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.108 AC: 16385 AN: 152160 Hom.: 2854 Cov.: 32 AF XY: 0.105 AC XY: 7797 AN XY: 74402

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.0359

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.000471

Gnomad4 NFE AF: 0.00356

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0525 Hom.: 367

Bravo AF: 0.121

Asia WGS AF: 0.0600 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7529671; hg19: chr1-97448929;