rs7539471

Variant names:

• chr1-65719720-G-A
• rs7539471

Your query was ambiguous. Multiple possible variants found:

• chr1-65719720-G-A
• chr1-65719720-G-T

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 0.257 in 152,146 control chromosomes in the GnomAD database, including 5,439 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 0.26 (5439 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.309 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: 0.257 AC: 39128 AN: 152028 Hom.: 5440 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.257 AC: 39143 AN: 152146 Hom.: 5439 Cov.: 31 AF XY: 0.253 AC XY: 18836 AN XY: 74372

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0237

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.263

Alfa AF: 0.298 Hom.: 14119

Bravo AF: 0.256

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7539471; hg19: chr1-66185403;