rs1065780

Positions:

• chr7-45888078-G-A

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 0.389 in 151,954 control chromosomes in the GnomAD database, including 11,731 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 0.39 (11731 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59090 AN: 151836 Hom.: 11710 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.389 AC: 59143 AN: 151954 Hom.: 11731 Cov.: 32 AF XY: 0.385 AC XY: 28555 AN XY: 74252

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.399

Alfa AF: 0.387 Hom.: 11767

Bravo AF: 0.401

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.065
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1065780; hg19: chr7-45927677;